An annotated table of 304 publications (2013–2026) using the ImageJ/Fiji plugin OrientationJ (Daniel Sage, Biomedical Imaging Group, EPFL) — with the sentence from each paper describing how it was used.
Most frequent fields: actin cytoskeleton (37), collagen/ECM in tumors (27), materials/nanofibers (27), cardiac tissue engineering (10), bone/mineralized tissue (5).
Click a column header to sort · 304 of 304 references shown
| # | Year | Reference | Field / application | OrientationJ mode | Usage extract (from the paper) |
|---|---|---|---|---|---|
| 1 | 2013 | Perry et al. (2013) Stromal matrix metalloprotease-13 knockout alters Collagen I structure at the tumor-host interface and increases lung metastasis of C57BL/6 syngeneic E0771 mammary tumor cells BMC Cancer · doi:10.1186/1471-2407-13-411 | collagen/ECM in tumors | Coherency | “the coherency parameter was calculated on these same collagen I IF images using the ImageJ plugin OrientationJ” |
| 2 | 2014 | Matis et al. (2014) Microtubules provide directional information for core PCP function eLife · doi:10.7554/elife.02893 | microtubule cytoskeleton, planar cell polarity | Color-coded orientation map | “Orientations of MTs, in the regions shown, calculated using OrientationJ, aligned with the P-D axis at each stage and location (arrows).” |
| 3 | 2014 | Zajączkowska (2014) Overgrowth of Douglas fir (Pseudotsuga menziesii Franco) stumps with regenerative tissue as an example of cell ordering and tissue reorganization Planta · doi:10.1007/s00425-014-2142-y | plant tissue regeneration and cell organization | Coherency and orientation analysis | “Cell ordering within the overgrowth tissue was estimated using the OrientationJ image analysis plugin based on structure tensor.” |
| 4 | 2014 | Li et al. (2014) Piezo1 integration of vascular architecture with physiological force Nature · doi:10.1038/nature13701 | vascular endothelial cell alignment | Distribution (directionality histogram) | “Automated quantification of cell orientation relative to the direction of shear stress was determined using OrientationJ software, also an ImageJ plugin” |
| 5 | 2015 | Pasqualini et al. (2015) Structural phenotyping of stem cell-derived cardiomyocytes Stem Cell Reports · doi:10.1016/j.stemcr.2015.01.020 | cardiac tissue engineering | orientation calculation | “OrientationJ ( Rezakhaniha et al., 2012 ) plugins were used to highlight the filamentous structure and calculate the orientations of foreground pixels, respectively.” |
| 6 | 2015 | Kalies et al. (2015) Investigation of biophysical mechanisms in gold nanoparticle mediated laser manipulation of cells using a multimodal holographic and fluorescence imaging setup PLOS ONE · doi:10.1371/journal.pone.0124052 | cell biophysics / gold nanoparticles | Coherency map | “This was done using the ImageJ plugin OrientationJ [ 38 , 39 ], that allows to measure the coherency of local image features.” |
| 7 | 2015 | Kartasalo et al. (2015) CytoSpectre: a tool for spectral analysis of oriented structures on cellular and subcellular levels BMC Bioinformatics · doi:10.1186/s12859-015-0782-y | cellular and subcellular oriented structures | Distribution (directionality histogram) | “Previously published general purpose tools include the ImageJ plug-ins FibrilTool and OrientationJ, which allow the quantification of orientation distributions based on intensity gradients.” |
| 8 | 2015 | Lee et al. (2015) In vivo imaging of the tumor and its associated microenvironment using combined CARS / 2-photon microscopy IntraVital · doi:10.1080/21659087.2015.1055430 | collagen/ECM in tumors | Coherency map | “Collagen coherency and amount was calculated from the left and right images via the OrientationJ plugin for ImageJ and thresholded area respectively.” |
| 9 | 2015 | Lin et al. (2015) Influence of Crosslink Density and Stiffness on Mechanical Properties of Type I Collagen Gel Materials · doi:10.3390/ma8020551 | collagen/ECM materials | orientation/coherency analysis | “The orientation of collagen fiber network was analyzed using the OrientationJ plugin [ 20 ] in ImageJ software (NIH, Bethesda, MD, USA).” |
| 10 | 2015 | Mitter et al. (2015) Validation of In utero Tractography of Human Fetal Commissural and Internal Capsule Fibers with Histological Structure Tensor Analysis Frontiers in Neuroanatomy · doi:10.3389/fnana.2015.00164 | fetal white matter tracts / neuronal fiber organization | structure-tensor order parameter | “ST analysis was performed with the OrientationJ plugin for ImageJ using a cubic spline gradient with a Gaussian window of 5 pix.” |
| 11 | 2015 | Hotaling et al. (2015) Dataset for the validation and use of DiameterJ an open source nanofiber diameter measurement tool Data in Brief · doi:10.1016/j.dib.2015.07.012 | materials/nanofibers | Distribution (directionality histogram) | “The file labeled " Figure 5 C – Orientation Histogram.xlsx" contains the frequency of occurrence of a given fiber orientation as defined by the OrientationJ plugin.” |
| 12 | 2015 | Jenkins et al. (2015) A nerve guidance conduit with topographical and biochemical cues: potential application using human neural stem cells Nanoscale Research Letters · doi:10.1186/s11671-015-0972-6 | materials/nanofibers | Distribution (directionality histogram) | “OrientationJ, a plug-in for ImageJ, was used to process SEM images and generate a table of pixels counted versus degree of orientation.” |
| 13 | 2015 | Bhadra et al. (2015) Antibacterial titanium nano-patterned arrays inspired by dragonfly wings Scientific Reports · doi:10.1038/srep16817 | materials/nanofibers | orientation/coherency analysis | “SEM images were obtained using the ImageJ ® 1.48 package with DiameterJ and OrientationJ plugins.” |
| 14 | 2015 | Zhang et al. (2015) Platform technology for scalable assembly of instantaneously functional mosaic tissues Science Advances · doi:10.1126/sciadv.1500423 | scaffold tissue engineering | orientation/coherency analysis | “Orientation of the scaffold struts was quantified using an ImageJ plug-in, OrientationJ” |
| 15 | 2015 | Breidenbach et al. (2015) Ablating hedgehog signaling in tenocytes during development impairs biomechanics and matrix organization of the adult murine patellar tendon enthesis Journal of Orthopaedic Research · doi:10.1002/jor.22899 | tendon/mineralized tissue biomechanics | Dominant Direction | “Collagen fiber orientation of the mineralized and unmineralized insertion was calculated using the FIJI plug‐in OrientationJ” |
| 16 | 2016 | Nesmith et al. (2016) A human in vitro model of Duchenne muscular dystrophy muscle formation and contractility Journal of Cell Biology · doi:10.1083/jcb.201603111 | actin cytoskeleton | Measure | “the orientation of actin fibers was determined using the OrientationJ plugin ( Rezakhaniha et al., 2012 ), and the actin OOP was calculated for each sample.” |
| 17 | 2016 | Squarr et al. (2016) Fat2 acts through the WAVE regulatory complex to drive collective cell migration during tissue rotation Journal of Cell Biology · doi:10.1083/jcb.201508081 | actin cytoskeleton | Distribution (directionality histogram) | “Rose plots show density distribution of local angles of actin bundles (calculated using OrientationJ).” |
| 18 | 2016 | Laksari et al. (2016) Energy-based constitutive modelling of local material properties of canine aortas Royal Society Open Science · doi:10.1098/rsos.160365 | cardiac tissue engineering | Dominant Direction | “OrientationJ determines the fibre directions in each area of interest by defining a weighted inner product and calculating the eigenvectors of the structure tensor” |
| 19 | 2016 | Sherratt et al. (2016) Raised mammographic density: causative mechanisms and biological consequences Breast Cancer Research · doi:10.1186/s13058-016-0701-9 | collagen/ECM in breast tissue | Color-coded orientation map | “Polarised light microscopy images of PSR-stained sections of c low and d high MD breast processed using the Image J plugin, OrientationJ.” |
| 20 | 2016 | McConnell et al. (2016) Increased peri-ductal collagen micro-organization may contribute to raised mammographic density Breast Cancer Research · doi:10.1186/s13058-015-0664-2 | collagen/ECM in breast tissue | Coherency map | “Polarised light microscopy of PSR-stained sections assessed using OrientationJ: e low MD, f high MD.” |
| 21 | 2016 | Kopanska et al. (2016) Tensile Forces Originating from Cancer Spheroids Facilitate Tumor Invasion PLOS ONE · doi:10.1371/journal.pone.0156442 | collagen/ECM in tumors | orientation/coherency analysis | “Collagen orientation was measured using "OrientationJ" plugin of ImageJ [ 56 ].” |
| 22 | 2016 | Chan et al. (2016) The Architecture of Iron Microbial Mats Reflects the Adaptation of Chemolithotrophic Iron Oxidation in Freshwater and Marine Environments Frontiers in Microbiology · doi:10.3389/fmicb.2016.00796 | microbial mat architecture | Measure | “Directionality measurements were taken using the ImageJ 2.0.0 OrientationJ Measure plugin” |
| 23 | 2016 | Koser et al. (2016) Mechanosensing is critical for axon growth in the developing brain Nature Neuroscience · doi:10.1038/nn.4394 | neuronal alignment in developing brain | orientation/coherency analysis | “These were analyzed using the OrientationJ plugin.” |
| 24 | 2016 | Bell et al. (2016) Microstructure and mechanics of human resistance arteries American Journal of Physiology-Heart and Circulatory Physiology · doi:10.1152/ajpheart.00002.2016 | vascular tissue mechanics | Distribution (directionality histogram) | “The OrientationJ Distribution plugin for Fiji ( 37 ) was used to quantify the orientation of the intimal and adventitial elastic fiber networks, and the collagen network.” |
| 25 | 2017 | Fritzsche et al. (2017) Cytoskeletal actin dynamics shape a ramifying actin network underpinning immunological synapse formation Science Advances · doi:10.1126/sciadv.1603032 | actin cytoskeleton | orientation and coherency analysis | “The orientation and isotropy properties of the actin filaments in a given region of an (experimental or simulated) image were computed based on the evaluation of the structure tensor in a local neighborhood using the Java plugin for ImageJ ( http://imagej.nih.gov/ ) "OrientationJ.” |
| 26 | 2017 | Wirshing et al. (2017) Myosin activity drives actomyosin bundle formation and organization in contractile cells of the Caenorhabditis elegans spermatheca Molecular Biology of the Cell · doi:10.1091/mbc.e17-01-0029 | actin cytoskeleton | Color-coded orientation map | “OrientationJ was used to false-color actin bundles according to their orientation in selected cells indicated by yellow boxes in A.” |
| 27 | 2017 | Horejs et al. (2017) Preventing tissue fibrosis by local biomaterials interfacing of specific cryptic extracellular matrix information Nature Communications · doi:10.1038/ncomms15509 | actin cytoskeleton | orientation/coherency analysis | “Actin fibre orientation was evaluated using the OrientationJ plug-in for ImageJ” |
| 28 | 2017 | Fritzsche et al. (2017) Self-organizing actin patterns shape membrane architecture but not cell mechanics Nature Communications · doi:10.1038/ncomms14347 | actin cytoskeleton | Measure | “The orientation and isotropy properties of a given region of interest in an image were computed based on the evaluation of the structure tensor in a local neighbourhood using the Java plug-in for ImageJ 'OrientationJ'.” |
| 29 | 2017 | Panzer et al. (2017) Nkx2-5 and Sarcospan genetically interact in the development of the muscular ventricular septum of the heart Scientific Reports · doi:10.1038/srep46438 | cardiac muscle myofibrils | orientation/coherency analysis | “The orientation of myofibers was analyzed using ImageJ and an ImageJ plugin, OrientationJ” |
| 30 | 2017 | Roy et al. (2017) Cancer cell chemokines direct chemotaxis of activated stellate cells in pancreatic ductal adenocarcinoma Laboratory Investigation · doi:10.1038/labinvest.2016.146 | collagen/ECM in tumors | orientation/coherency analysis | “ECM fiber orientation analysis Monochromatic images corresponding to fibronectin fiber acquisitions were analyzed via ImageJ's OrientationJ plugin” |
| 31 | 2017 | Franco-Barraza et al. (2017) Matrix-regulated integrin αvβ5 maintains α5β1-dependent desmoplastic traits prognostic of neoplastic recurrence eLife · doi:10.7554/elife.20600 | collagen/ECM in tumors | Color-coded orientation map | “ECM fiber angle distributions, measured with Image-J's 'OrientationJ' plug, are represented by the various colors” |
| 32 | 2017 | Lombardo et al. (2017) Multimodal imaging quality control of epithelia regenerated with cultured human donor corneal limbal epithelial stem cells Scientific Reports · doi:10.1038/s41598-017-05486-8 | corneal epithelial tissue engineering | Coherency map | “The plugin OrientationJ in ImageJ was used for analysis of stromal collagen fiber orientations, based on the evaluation of the structure tensor in a local neighborhood” |
| 33 | 2017 | Gouveia et al. (2017) Controlling the 3D architecture of Self-Lifting Auto-generated Tissue Equivalents (SLATEs) for optimized corneal graft composition and stability Biomaterials · doi:10.1016/j.biomaterials.2016.12.023 | corneal tissue engineering, collagen organization | Measure | “Data was analyzed using the OrientationJ plugin from ImageJ v1.46 for measuring collagen fibril dimensions, orientation, and distribution.” |
| 34 | 2017 | Chen et al. (2017) Direct Writing Electrospinning of Scaffolds with Multidimensional Fiber Architecture for Hierarchical Tissue Engineering ACS Applied Materials & Interfaces · doi:10.1021/acsami.7b07151 | electrospun nanofiber scaffolds | orientation/coherency analysis | “The plugin OrientationJ was employed for this purpose, and the images were analyzed over the same ROI.” |
| 35 | 2017 | Webster et al. (2017) Upregulated WEE1 protects endothelial cells of colorectal cancer liver metastases Oncotarget · doi:10.18632/oncotarget.15039 | endothelial cell alignment in tumors | Distribution (directionality histogram) | “Quantification of cell orientation relative to the direction of shear stress was determined using OrientationJ software” |
| 36 | 2017 | Saw et al. (2017) Topological defects in epithelia govern cell death and extrusion Nature · doi:10.1038/nature21718 | epithelial tissue organization | structure tensor eigenvector direction | “OrientationJ was used to detect the direction of largest eigenvector of the structure tensor of the image for each pixel” |
| 37 | 2017 | Marrero et al. (2017) Fibroblast reticular cells engineer a blastema extracellular network during digit tip regeneration in mice Regeneration · doi:10.1002/reg2.75 | extracellular matrix/tissue regeneration | Vector Field | “measuring vectors in 32‐bit thresholded channels of ER‐TR7 + staining using the OrientationJ plugin” |
| 38 | 2017 | Gnilitskyi et al. (2017) High-speed manufacturing of highly regular femtosecond laser-induced periodic surface structures: physical origin of regularity Scientific Reports · doi:10.1038/s41598-017-08788-z | materials/laser-induced surface structures | Distribution (directionality histogram) | “different spectra ( b ) of orientations θ can be obtained with the module OrientationJ 23 of the open software ImageJ 59” |
| 39 | 2017 | Modarres et al. (2017) Neural Network for Nanoscience Scanning Electron Microscope Image Recognition Scientific Reports · doi:10.1038/s41598-017-13565-z | materials/nanofibers | Coherency map | “The scores for the aligned category by image classification are compared with a normalised value for alignment (coherency) using the OrientationJ plugin on ImageJ.” |
| 40 | 2017 | Chou et al. (2017) Relationships between mechanical properties and drug release from electrospun fibers of PCL and PLGA blends Journal of the Mechanical Behavior of Biomedical Materials · doi:10.1016/j.jmbbm.2016.09.004 | materials/nanofibers | Coherency map | “Image analysis was carried out by image processing software (ImageJ, National Institutes of Health, Bethesda, MD, USA) using OrientationJ plugin for fiber alignment measurement by applying a Riesz filter at 70% minimal coherency and 2% minimal energy.” |
| 41 | 2017 | Gatta et al. (2017) Modulating the metabolism by trimetazidine enhances myoblast differentiation and promotes myogenesis in cachectic tumor-bearing c26 mice Oncotarget · doi:10.18632/oncotarget.23044 | muscle myoblast differentiation | Distribution (directionality histogram) | “A segment crossing the longest part of each cell was added and used to analyze the distribution of cell direction by the OrientationJ (Distribution) plug-in of Image J.” |
| 42 | 2017 | Costantini et al. (2017) Engineering Muscle Networks in 3D Gelatin Methacryloyl Hydrogels: Influence of Mechanical Stiffness and Geometrical Confinement Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2017.00022 | muscle tissue engineering | Distribution (directionality histogram) | “The distributions of myotube orientation within the hydrogel structures following in vitro culture was obtained by analyzing IF micrographs (MHC signal) with OrientationJ plugin” |
| 43 | 2017 | Peng et al. (2017) Nerve guidance conduit with a hybrid structure of a PLGA microfibrous bundle wrapped in a micro/nanostructured membrane International Journal of Nanomedicine · doi:10.2147/ijn.s122017 | nerve guidance conduit / neural tissue engineering | orientation/coherency analysis | “used ImageJ and OrientationJ software to estimate cell length and growth direction, respectively” |
| 44 | 2017 | Kim et al. (2017) Anisotropically organized three-dimensional culture platform for reconstruction of a hippocampal neural network Nature Communications · doi:10.1038/ncomms14346 | neuronal alignment in hippocampal tissue engineering | Color-coded orientation map | “OrientationJ plug-in of ImageJ software was used for quantitative analyses of confocal fluorescence images.” |
| 45 | 2017 | Rose et al. (2017) Nerve Cells Decide to Orient inside an Injectable Hydrogel with Minimal Structural Guidance Nano Letters · doi:10.1021/acs.nanolett.7b01123 | neuronal alignment in hydrogels | Distribution (directionality histogram) | “The orientation time was determined via a software-based orientation analysis (ImageJ plugin OrientationJ), which evaluated every pixel of the image based on a structure tensor” |
| 46 | 2017 | van et al. (2017) A quantitative method for microstructural analysis of myelinated axons in the injured rodent brain Scientific Reports · doi:10.1038/s41598-017-16797-1 | white matter microstructure, injured brain | Coherency measure | “Coherency of myelinated axons, as an inverse measure of complexity of white matter microstructure, was assessed using the 'OrientationJ measure' function” |
| 47 | 2018 | Kelley et al. (2018) The myosin light-chain kinase MLCK-1 relocalizes during Caenorhabditis elegans ovulation to promote actomyosin bundle assembly and drive contraction Molecular Biology of the Cell · doi:10.1091/mbc.e18-01-0056 | actin cytoskeleton | Color-coded orientation map | “OrientationJ ( Rezakhaniha et al. , 2012 ), configured using a Gaussian fit with a pixel size of 2, was used to measure the orientation distribution of actin bundles in individual cells and to generate color-coded images where color indicates orientation, hue indicates coherency, and brightness is the brightness of…” |
| 48 | 2018 | Cascione et al. (2018) Transforming Growth Factor-β Promotes Morphomechanical Effects Involved in Epithelial to Mesenchymal Transition in Living Hepatocellular Carcinoma International Journal of Molecular Sciences · doi:10.3390/ijms20010108 | actin cytoskeleton | Coherency map | “the actin fiber coherency parameter was quantified using the OrientationJ plugin” |
| 49 | 2018 | Wirshing et al. (2018) Spectrin regulates cell contractility through production and maintenance of actin bundles in the Caenorhabditis elegans spermatheca Molecular Biology of the Cell · doi:10.1091/mbc.e18-06-0347 | actin cytoskeleton | Color-coded orientation map | “OrientationJ ( Rezakhaniha et al. , 2012 ), configured using a Gaussian fit with a pixel size of 2, was used to measure the orientation distribution of actin bundles in individual cells and to generate color-coded images where color indicates orientation, hue indicates coherency, and brightness is the brightness of…” |
| 50 | 2018 | Pandey et al. (2018) Cardiomyocytes Sense Matrix Rigidity through a Combination of Muscle and Non-muscle Myosin Contractions Developmental Cell · doi:10.1016/j.devcel.2017.12.024 | actin cytoskeleton, muscle myofibrils | Color-coded orientation map | “Actin and α-actinin images of single cells were then analysed for filament alignment using the OrientationJ plugin for ImageJ” |
| 51 | 2018 | Petersen et al. (2018) A biomaterial with a channel-like pore architecture induces endochondral healing of bone defects Nature Communications · doi:10.1038/s41467-018-06504-7 | bone/mineralized tissue | Distribution (directionality histogram) | “Distribution of fiber orientation was analyzed via the ImageJ plug-in OrientationJ (by Daniel Sage) on two to three technical replicates (scaffolds) and three confocal image stacks per scaffold.” |
| 52 | 2018 | Hansen et al. (2018) Development of a Contractile Cardiac Fiber From Pluripotent Stem Cell Derived Cardiomyocytes Frontiers in Cardiovascular Medicine · doi:10.3389/fcvm.2018.00052 | cardiac tissue engineering | Dominant Direction | “Alpha-Actinin Fiber Alignment Confocal images of alpha-actinin stained hPS-CM seed on microthreads and TCP were uploaded to ImageJ (NIH) for actinin fiber alignment using OrientationJ.” |
| 53 | 2018 | Duclos et al. (2018) Spontaneous shear flow in confined cellular nematics Nature Physics · doi:10.1038/s41567-018-0099-7 | cellular nematics, liquid crystals | structure tensor | “The orientation field was obtained by computing the local structure tensor with ImageJ plugin OrientationJ” |
| 54 | 2018 | Clemons et al. (2018) Coherency image analysis to quantify collagen architecture: implications in scar assessment RSC Advances · doi:10.1039/c7ra12693j | collagen architecture in scar tissue | Coherency map | “the OrientationJ plugin gives a value for coherency without the disadvantages previously discussed involving the Gaussian fit” |
| 55 | 2018 | Ashworth et al. (2018) Optimising collagen scaffold architecture for enhanced periodontal ligament fibroblast migration Journal of Materials Science: Materials in Medicine · doi:10.1007/s10856-018-6175-9 | collagen scaffold tissue engineering | Dominant Direction | “The OrientationJ plugin in FIJI was used to quantify the collagen pore wall orientation from bright field images taken of the scaffold cross-sections.” |
| 56 | 2018 | Kinugasa et al. (2018) A Multi-modality Approach Towards Elucidation of the Mechanism for Human Achilles Tendon Bending During Passive Ankle Rotation Scientific Reports · doi:10.1038/s41598-018-22661-7 | collagen/ECM in tendon tissue | Coherency map | “The local collagen fiber alignment was determined with the ImageJ plug-in OrientationJ (Version 19.11.2012., available online at http://bigwww.epfl.ch/demo/orientation/ )” |
| 57 | 2018 | Zanotelli et al. (2018) Regulation of ATP utilization during metastatic cell migration by collagen architecture Molecular Biology of the Cell · doi:10.1091/mbc.e17-01-0041 | collagen/ECM in tumors | orientation/coherency analysis | “Fiber orientation was then analyzed in ImageJ using OrientationJ.” |
| 58 | 2018 | Martin et al. (2018) Control of endothelial cell polarity and sprouting angiogenesis by non-centrosomal microtubules eLife · doi:10.7554/elife.33864 | endothelial cell cytoskeleton | Orientation angle map | “local orientation angle map was calculated for each pixel using OrientationJ plugin ( Püspöki et al., 2016 ).” |
| 59 | 2018 | Morley et al. (2018) Piezo1 channels are mechanosensors in human fetoplacental endothelial cells MHR: Basic science of reproductive medicine · doi:10.1093/molehr/gay033 | endothelial cell cytoskeleton under shear stress | Dominant Direction | “OrientationJ plugin37 quantified cell orientation relative to the direction of shear stress” |
| 60 | 2018 | Skrzypek et al. (2018) An important step towards a prevascularized islet macroencapsulation device-effect of micropatterned membranes on development of endothelial cell network Journal of Materials Science: Materials in Medicine · doi:10.1007/s10856-018-6102-0 | endothelial cell network tissue engineering | Dominant Direction | “The orientation of skeletonized HUVEC structures relative to surface topography (x-axis) was quantified using the OrientationJ plugin.” |
| 61 | 2018 | Krishnamoorthy et al. (2018) Dietary advanced glycation end-product consumption leads to mechanical stiffening of murine intervertebral discs Disease Models & Mechanisms · doi:10.1242/dmm.036012 | intervertebral disc collagen/ECM | Collagen orientation quantification | “Collagen orientation was quantified from the B-SHG images using OrientationJ, a series of plugins for ImageJ” |
| 62 | 2018 | Rychter et al. (2018) Cilostazol-Loaded Poly(ε-Caprolactone) Electrospun Drug Delivery System for Cardiovascular Applications Pharmaceutical Research · doi:10.1007/s11095-017-2314-0 | materials/nanofibers | structure tensor | “Visual orientation analysis was conducted by OrientationJ and involved the structure tensor calculations for each pixel in the SEM image.” |
| 63 | 2018 | Bleck et al. (2018) Subcellular connectomic analyses of energy networks in striated muscle Nature Communications · doi:10.1038/s41467-018-07676-y | muscle mitochondrial network organization | Distribution (directionality histogram) | “the OrientationJ Distributions plugin was used to determine the angles of the mitochondrial network” |
| 64 | 2018 | van et al. (2018) Combined fetal inflammation and postnatal hypoxia causes myelin deficits and autism-like behavior in a rat model of diffuse white matter injury Glia · doi:10.1002/glia.23216 | neuronal alignment in white matter | Coherency map | “Coherency of NF200 + axons was measured using the OrientationJ plugin for ImageJ (Fonck et al., 2009 ).” |
| 65 | 2018 | Morawski et al. (2018) Developing 3D microscopy with CLARITY on human brain tissue: Towards a tool for informing and validating MRI-based histology NeuroImage · doi:10.1016/j.neuroimage.2017.11.060 | neuronal fiber alignment in brain | structure tensor algorithm | “the in-plane orientation of fiber structures was obtained from the probability maps using the local edge orientation computed by the Directionality module in FIJI or alternatively using the estimation of local structure tensor algorithm implemented in OrientationJ” |
| 66 | 2018 | Kobayashi et al. (2018) Bioengineering functional smooth muscle with spontaneous rhythmic contraction in vitro Scientific Reports · doi:10.1038/s41598-018-31992-4 | smooth muscle tissue engineering | Coherency map | “the plugin OrientationJ was used to conduct coherency analysis (Kit, MHC, GFP and β-tubulin)” |
| 67 | 2018 | Gurevich et al. (2018) Live imaging of wound angiogenesis reveals macrophage orchestrated vessel sprouting and regression The EMBO Journal · doi:10.15252/embj.201797786 | vessel/vascular tissue | Coherency map | “Vessel orientation was measured using the ImageJ plugin OrientationJ, which rates the coherence of neighbouring pixels between 0 (isotropic, no overall direction) and 1 (one dominant direction; Fonck et al , 2009 ).” |
| 68 | 2019 | Colin-York et al. (2019) Cytoskeletal actin patterns shape mast cell activation Communications Biology · doi:10.1038/s42003-019-0322-9 | actin cytoskeleton | Distribution (directionality histogram) | “Using the 'OrientationJ' Java plugin for ImageJ, the distribution of fiber orientations within a region of interested was evaluated” |
| 69 | 2019 | Fearing et al. (2019) Mechanosensitive transcriptional coactivators MRTF-A and YAP/TAZ regulate nucleus pulposus cell phenotype through cell shape The FASEB Journal · doi:10.1096/fj.201802725rrr | actin cytoskeleton | orientation analysis | “F-actin orientation was analyzed from microscopic images (ImageJ plugin, OrientationJ).” |
| 70 | 2019 | Cascione et al. (2019) Acute Cytotoxic Effects on Morphology and Mechanical Behavior in MCF-7 Induced by TiO2NPs Exposure International Journal of Molecular Sciences · doi:10.3390/ijms20143594 | actin cytoskeleton | Coherency | “The cytoskeletal actin organization was characterized in terms of coherency by means of OrientationJ plugin (ImageJ software)” |
| 71 | 2019 | Fanalista et al. (2019) Shape and Size Control of Artificial Cells for Bottom-Up Biology ACS Nano · doi:10.1021/acsnano.9b00220 | artificial cells, tubulin and collagen | orientation/coherency analysis | “the values of tubulin and collagen bundle orientations were obtained using Fiji (OrientationJ plugin) after the background was appropriately subtracted” |
| 72 | 2019 | Yaman et al. (2019) Emergence of active nematics in chaining bacterial biofilms Nature Communications · doi:10.1038/s41467-019-10311-z | bacterial biofilm active matter | Vector Field | “The ImageJ plugin OrientationJ was used to find the nematic director field of the colony.” |
| 73 | 2019 | Shkarin et al. (2019) Quanfima: An open source Python package for automated fiber analysis of biomaterials PLOS ONE · doi:10.1371/journal.pone.0215137 | biomaterials fiber analysis | orientation/coherency analysis | “The OrientationJ plug-in is aimed initially at the analysis of microscopy images and provides information about orientation, coherency, and energy within a specified ROI.” |
| 74 | 2019 | Gonzalez-Molina et al. (2019) The extracellular fluid macromolecular composition differentially affects cell-substrate adhesion and cell morphology Scientific Reports · doi:10.1038/s41598-019-44960-3 | cell morphology and adhesion | Color-coded orientation map | “Pseudo-coloured images were obtained with the OrientationJ plugin of ImageJ using a Gaussian window of 2 pixels, a Fourier gradient, and colours representing orientation (hue) and coherency (saturation).” |
| 75 | 2019 | De et al. (2019) Tailoring Cell Morphomechanical Perturbations Through Metal Oxide Nanoparticles Nanoscale Research Letters · doi:10.1186/s11671-019-2941-y | cell morphomechanics, nanoparticle effects | Coherency map | “OrientationJ plugin was used to quantify the coherency parameter by choosing a specific sequence of ROIs in confocal acquisitions, based on the measure of the structure tensors in a local neighborhood.” |
| 76 | 2019 | Taufalele et al. (2019) Fiber alignment drives changes in architectural and mechanical features in collagen matrices PLOS ONE · doi:10.1371/journal.pone.0216537 | collagen/ECM biomaterial engineering | Color-coded orientation map, Coherency map, Distribution (directionality histogram) | “To measure the alignment of the collagen matrices, confocal reflectance images were analyzed via the OrientationJ plugin in ImageJ” |
| 77 | 2019 | Reed et al. (2019) Two-photon fluorescence and second harmonic generation characterization of extracellular matrix remodeling in post-injury murine temporomandibular joint osteoarthritis PLOS ONE · doi:10.1371/journal.pone.0214072 | collagen/ECM in joint osteoarthritis | Measure | “All data was collected using the OrientationJ plugin [ 52 ] and collagen orientation measurements follow published methods [ 53 ].” |
| 78 | 2019 | Jones et al. (2019) Stromal PTEN Regulates Extracellular Matrix Organization in the Mammary Gland Neoplasia · doi:10.1016/j.neo.2018.10.010 | collagen/ECM in mammary tissue | orientation/coherency analysis | “The maximum intensity projection of these images was analyzed with the OrientationJ plugin for ImageJ [26] , which analyzes fiber orientation on a pixel-by-pixel basis” |
| 79 | 2019 | Desa et al. (2019) Second-harmonic generation directionality is associated with neoadjuvant chemotherapy response in breast cancer core needle biopsies Journal of Biomedical Optics · doi:10.1117/1.jbo.24.8.086503 | collagen/ECM in tumors | Coherency map | “Coherency-based F/B was calculated from tumor bulk and tumor–host interface in each HER2+ core needle biopsy ( n = 29 ) using OrientationJ.” |
| 80 | 2019 | Natal et al. (2019) Exploring Collagen Parameters in Pure Special Types of Invasive Breast Cancer Scientific Reports · doi:10.1038/s41598-019-44156-9 | collagen/ECM in tumors | orientation/coherency analysis | “Quantitative analysis of collagen parameters was performed in SHG images using ImageJ and OrientationJ plug-in” |
| 81 | 2019 | Nguyen et al. (2019) Proteomic Profiling of Human Prostate Cancer-associated Fibroblasts (CAF) Reveals LOXL2-dependent Regulation of the Tumor Microenvironment Molecular & Cellular Proteomics · doi:10.1074/mcp.ra119.001496 | collagen/ECM in tumors | orientation/coherency analysis | “The orientation of ECM fibers was analyzed using ImageJ (NIH) plugin OrientationJ as previously described” |
| 82 | 2019 | Sheen et al. (2019) Replication Study: Biomechanical remodeling of the microenvironment by stromal caveolin-1 favors tumor invasion and metastasis eLife · doi:10.7554/elife.45120 | collagen/ECM in tumors | Coherency | “coherency, the degree to which the local features are oriented, was measured with OrientationJ ( Rezakhaniha et al., 2012 )” |
| 83 | 2019 | Zeltz et al. (2019) LOXL1 Is Regulated by Integrin α11 and Promotes Non-Small Cell Lung Cancer Tumorigenicity Cancers · doi:10.3390/cancers11050705 | collagen/ECM in tumors | orientation/coherency analysis | “Alignment of collagen fibers in the remodeled matrix was recorded using second harmonic generation and analyzed with OrientationJ.” |
| 84 | 2019 | Gârlea et al. (2019) Colloidal Liquid Crystals Confined to Synthetic Tactoids Scientific Reports · doi:10.1038/s41598-019-56729-9 | colloidal liquid crystals, tactoids | orientation/coherency analysis | “The local alignment is determined using the plug-in "OrientationJ" of "ImageJ".” |
| 85 | 2019 | Ferrando et al. (2019) Secondary Folds Contribute Significantly to the Total Surface Area in the Olfactory Organ of Chondrichthyes Frontiers in Physiology · doi:10.3389/fphys.2019.00245 | fish olfactory organ morphology | Harris corner detection (with OrientationJ for image analysis support) | “this count was performed individuating the Harris corners (by an algorithm) in the lamellae silhouettes using the OrientationJ plug-in for ImageJ” |
| 86 | 2019 | Liverani et al. (2019) Electrospun patterned porous scaffolds for the support of ovarian follicles growth: a feasibility study Scientific Reports · doi:10.1038/s41598-018-37640-1 | materials/nanofibers | average fiber diameter and porosity analysis | “The calculation of the average fiber diameter and the analysis of the porosity were performed by using ImageJ and its plugins (DiameterJ and OrientationJ)” |
| 87 | 2019 | MacQueen et al. (2019) Muscle tissue engineering in fibrous gelatin: implications for meat analogs npj Science of Food · doi:10.1038/s41538-019-0054-8 | muscle tissue engineering, meat analogs | Orientation/coherency analysis | “Analysis of fiber diameter and alignment ImageJ software (NIH) with the DiameterJ and OrientationJ plug-ins was used to determine fiber diameter and alignment from the SEM images” |
| 88 | 2019 | Giandomenico et al. (2019) Cerebral organoids at the air-liquid interface generate diverse nerve tracts with functional output Nature Neuroscience · doi:10.1038/s41593-019-0350-2 | neuronal alignment in cerebral organoids | Coherency map; Color-coded orientation map | “The product of OrientationJ coherency and energy output levels was quantified in whole organoids compared with ALI-COs, demonstrating more aligned structures.” |
| 89 | 2019 | Beber et al. (2019) Membrane reshaping by micrometric curvature sensitive septin filaments Nature Communications · doi:10.1038/s41467-019-08344-5 | septin filaments, membrane structure | orientation | “SEM images were analyzed using OrientationJ (a plug-in for imageJ) to determine the orientation of the filaments” |
| 90 | 2020 | Layton et al. (2020) Single cell force profiling of human myofibroblasts reveals a biophysical spectrum of cell states Biology Open · doi:10.1242/bio.049809 | actin cytoskeleton | Coherency map | “The orientation properties of the actin filaments in myofibroblast immunofluorescence images (Phalloidin-488) were computed based on the evaluation of the structure tensor in a local neighbourhood using the Java plugin for ImageJ 'OrientationJ'.” |
| 91 | 2020 | Rougerie et al. (2020) Topographical curvature is sufficient to control epithelium elongation Scientific Reports · doi:10.1038/s41598-020-70907-0 | actin cytoskeleton | Coherency map | “We quantified the average spatial orientation of actin fibers in confocal z-stack using OrientationJ Fiji plugin 25 and we observed that the anisotropic density of F-actin was accompanied with a curvature-dependent longitudinal alignment” |
| 92 | 2020 | Xu et al. (2020) Nesfatin-1 Promotes the Osteogenic Differentiation of Tendon-Derived Stem Cells and the Pathogenesis of Heterotopic Ossification in Rat Tendons via the mTOR Pathway Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2020.547342 | actin cytoskeleton | orientation/coherency analysis | “The anisotropy of actin fibers was measured using OrientationJ plug-in for ImageJ to evaluate the arrangement of stress fibers.” |
| 93 | 2020 | Owens et al. (2020) Lamin-Related Congenital Muscular Dystrophy Alters Mechanical Signaling and Skeletal Muscle Growth International Journal of Molecular Sciences · doi:10.3390/ijms22010306 | actin cytoskeleton, skeletal muscle | Dominant Direction | “Actin fiber coherence in the dominant direction as determined by analysis of confocal images of myotubes stained fluorescently for actin (phalloidin) in ImageJ using OrientationJ plug-in.” |
| 94 | 2020 | Weiss et al. (2020) Mechanics-driven mechanobiological mechanisms of arterial tortuosity Science Advances · doi:10.1126/sciadv.abd3574 | arterial tissue mechanics | Distribution (directionality histogram) | “the in-plane distribution of orientations was estimated using a 2D structure tensor analysis with OrientationJ implemented for ImageJ.” |
| 95 | 2020 | Sullivan et al. (2020) Transplantation of induced neural stem cells (iNSCs) into chronically demyelinated corpus callosum ameliorates motor deficits Acta Neuropathologica Communications · doi:10.1186/s40478-020-00960-3 | astrocyte and myelin alignment | structure tensor analysis | “OrientationJ Plug-in (RRID:SCR_014796, http://bigwww.epfl.ch/demo/orientation/ ) was used for structure tensor analysis” |
| 96 | 2020 | Lim et al. (2020) Aligned Nanofiber-Guided Bone Regeneration Barrier Incorporated with Equine Bone-Derived Hydroxyapatite for Alveolar Bone Regeneration Polymers · doi:10.3390/polym13010060 | bone/mineralized tissue | Distribution (directionality histogram) | “aligned scaffolds showed a distribution of orientations concentrated over 1000 in certain degree orientations, while random patterned scaffolds showed a distribution of orientations under 1000 with varying degree orientations” |
| 97 | 2020 | Chanthra et al. (2020) A Novel Fluorescent Reporter System Identifies Laminin-511/521 as Potent Regulators of Cardiomyocyte Maturation Scientific Reports · doi:10.1038/s41598-020-61163-3 | cardiac myofibril alignment | Distribution (directionality histogram) | “immunofluorescent images for α-actinin were transformed into frequency spectrum images for the evaluation of the distributions of orientation frequencies by OrientationJ” |
| 98 | 2020 | Tsukamoto et al. (2020) Vascularized cardiac tissue construction with orientation by layer-by-layer method and 3D printer Scientific Reports · doi:10.1038/s41598-020-59371-y | cardiac tissue engineering | orientation/coherency analysis | “ImageJ plug-in, OrientationJ, was used for the quantification of the fabricated 3D tissue's cell orientation” |
| 99 | 2020 | Zouhair et al. (2020) A Comprehensive Comparison of Bovine and Porcine Decellularized Pericardia: New Insights for Surgical Applications Biomolecules · doi:10.3390/biom10030371 | cardiac tissue engineering | Coherency | “Coherency, i.e., C, was calculated for collagen and elastin to verify the local dominant orientation in representative regions of interest (n = 9) using OrientationJ” |
| 100 | 2020 | Sharifi et al. (2020) Angiotensin Receptor-Neprilysin Inhibition Attenuates Right Ventricular Remodeling in Pulmonary Hypertension Journal of the American Heart Association · doi:10.1161/jaha.119.015708 | cardiac tissue, pulmonary hypertension | orientation/coherency analysis | “Image processing and fiber orientation analysis were performed using the OrientationJ toolbox in ImageJ” |
| 101 | 2020 | Feld et al. (2020) Cellular contractile forces are nonmechanosensitive Science Advances · doi:10.1126/sciadv.aaz6997 | cellular contractile forces and cytoskeleton | orientation/coherency analysis | “Fiber orientation analysis was performed using the Ridge Detection and OrientationJ plugins for Fiji.” |
| 102 | 2020 | Lu et al. (2020) Longitudinal optical coherence tomography imaging of tissue repair and microvasculature regeneration and function after targeted cerebral ischemia Journal of Biomedical Optics · doi:10.1117/1.jbo.25.4.046002 | cerebral ischemia tissue repair and microvasculature | Color-coded orientation map | “Local orientation and coherence were computed for each pixel of the filter-enhanced 2-D en face angiogram based on its structure tensor using OrientationJ” |
| 103 | 2020 | Liu et al. (2020) Fibrillar Collagen Quantification With Curvelet Transform Based Computational Methods Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2020.00198 | collagen/ECM in tissue | Coherency map | “the alignment for OrientationJ uses the coherency calculated in the tool, while the alignment for CytoSpectre equals 1 - circular variance of the orientations.” |
| 104 | 2020 | Hoang et al. (2020) ERK5 Is Required for Tumor Growth and Maintenance Through Regulation of the Extracellular Matrix in Triple Negative Breast Cancer Frontiers in Oncology · doi:10.3389/fonc.2020.01164 | collagen/ECM in tumors | Distribution (directionality histogram) | “the FIJI plugins DiameterJ and OrientationJ were used to generate data on the distributions of fiber diameter, orientation, and pore size” |
| 105 | 2020 | Jaeschke et al. (2020) Cancer-associated fibroblasts of the prostate promote a compliant and more invasive phenotype in benign prostate epithelial cells Materials Today Bio · doi:10.1016/j.mtbio.2020.100073 | collagen/ECM in tumors | Distribution (directionality histogram) | “The OrientationJ plugin in Fiji (ImageJ 1.52p) was used for orientation distribution analysis.” |
| 106 | 2020 | Druzhkova et al. (2020) Expression of EMT-Related Genes in Hybrid E/M Colorectal Cancer Cells Determines Fibroblast Activation and Collagen Remodeling International Journal of Molecular Sciences · doi:10.3390/ijms21218119 | collagen/ECM in tumors | orientation/coherency analysis | “Quantitative analysis of the SHG signal was performed using ImageJ software (National Institutes of Health, Bethesda, MD, USA) and the OrientationJ plugin.” |
| 107 | 2020 | Lucchetti et al. (2020) CD147 Promotes Cell Small Extracellular Vesicles Release during Colon Cancer Stem Cells Differentiation and Triggers Cellular Changes in Recipient Cells Cancers · doi:10.3390/cancers12020260 | extracellular vesicles in colon cancer | Coherency map | “Analyses were performed using the OrientationJ plugins to analyze the coherency” |
| 108 | 2020 | Natan et al. (2020) Long-range mechanical coupling of cells in 3D fibrin gels Molecular Biology of the Cell · doi:10.1091/mbc.e20-01-0079 | fibrin ECM and cell mechanotransduction | Distribution (directionality histogram) | “Orientation distribution of the fibrous matrix between cell pairs was conducted based on 2D images, using ImageJ with the ImageJ plug-in, OrientationJ” |
| 109 | 2020 | Hashimoto et al. (2020) The effects of coating culture dishes with collagen on fibroblast cell shape and swirling pattern formation Journal of Biological Physics · doi:10.1007/s10867-020-09556-3 | fibroblast cell alignment and ECM | Color-coded orientation map | “These images were analysed with the ImageJ plugin OrientationJ [ 19 ] to generate the colour-coded maps shown in Fig.” |
| 110 | 2020 | Michalaki et al. (2020) Perpendicular alignment of lymphatic endothelial cells in response to spatial gradients in wall shear stress Communications Biology · doi:10.1038/s42003-019-0732-8 | lymphatic endothelial cell alignment | Measure | “0, 6, 12, 18, and 24 h, using the OrientationJ Measure plugin in Fiji for 50 cells per binned region.” |
| 111 | 2020 | Andrzejewski et al. (2020) The Influence of the Hybridization Process on the Mechanical and Thermal Properties of Polyoxymethylene (POM) Composites with the Use of a Novel Sustainable Reinforcing System Based on Biocarbon and Basalt Fiber (BC/BF) Materials · doi:10.3390/ma13163496 | materials/nanofibers | orientation/coherency analysis | “Basalt fiber arrangement was analyzed using the OrientationJ plugin, where the task of this software is to characterize the orientation in the image based on the evaluation of the structure tensor in the local neighborhood.” |
| 112 | 2020 | Kaneko et al. (2020) Different motilities of microtubules driven by kinesin-1 and kinesin-14 motors patterned on nanopillars Science Advances · doi:10.1126/sciadv.aax7413 | microtubule motor protein dynamics | Measure | “Using OrientationJ, the angles were calculated for each pixel of the fluorescence images of the microtubules.” |
| 113 | 2020 | Colin et al. (2020) Cortical tension overrides geometrical cues to orient microtubules in confined protoplasts Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2008895117 | plant cell microtubule cytoskeleton | Dominant Direction | “We first calculated a mean CMT orientation per protoplast, with the OrientationJ, Dominant Direction plugin, and second, we calculated a deformation ratio” |
| 114 | 2020 | Jensen et al. (2020) Large-scale spontaneous self-organization and maturation of skeletal muscle tissues on ultra-compliant gelatin hydrogel substrates Scientific Reports · doi:10.1038/s41598-020-69936-6 | skeletal muscle myofibrils | Color-coded orientation map | “Composite images were composed of 252 frames, and the OrientationJ ImageJ plug-in was used to false-color the image according to the local angle of orientation of F-actin filaments.” |
| 115 | 2020 | Velasco-Mallorquí et al. (2020) New volumetric CNT-doped gelatin-cellulose scaffolds for skeletal muscle tissue engineering Nanoscale Advances · doi:10.1039/d0na00268b | skeletal muscle tissue engineering | Distribution (directionality histogram) | “The ImageJ PlugIn "OrientationJ" software was used to see the distribution of the aligned fibers and the alignment of the cells in a random fiber distribution of the cryogel against the anisotropic cryogels.” |
| 116 | 2020 | Adamowicz et al. (2020) Development of a conductive biocomposite combining graphene and amniotic membrane for replacement of the neuronal network of tissue-engineered urinary bladder Scientific Reports · doi:10.1038/s41598-020-62197-3 | smooth muscle cell alignment, tissue engineering | Measure | “The orientation of cultivated SMC was established by a square ROI (80 × 80 pixels) (n = 10) analysis using ImageJ OrientationJ (EPFL, Switzerland) plugin.” |
| 117 | 2020 | Talò et al. (2020) Independent, Controllable Stretch-Perfusion Bioreactor Chambers to Functionalize Cell-Seeded Decellularized Tendons Annals of Biomedical Engineering · doi:10.1007/s10439-019-02257-6 | tendon tissue engineering, collagen alignment | Coherency map | “To quantify the coherency and the local alignment of the new collagen deposition within the inner injected channels, ImageJ plug-in OrientationJ (Version 19.11.2012) was employed.” |
| 118 | 2021 | De et al. (2021) Physico-Chemical Properties of Inorganic NPs Influence the Absorption Rate of Aquatic Mosses Reducing Cytotoxicity on Intestinal Epithelial Barrier Model Molecules · doi:10.3390/molecules26102885 | actin cytoskeleton | Coherency map | “Coherency values of F-actin were performed on 20 cells, using the OrientationJ plugin of the ImageJ 1.47 software.” |
| 119 | 2021 | De et al. (2021) Synergistic Effect Induced by Gold Nanoparticles with Polyphenols Shell during Thermal Therapy: Macrophage Inflammatory Response and Cancer Cell Death Assessment Cancers · doi:10.3390/cancers13143610 | actin cytoskeleton | Coherency map | “Morphometric quantification (coherency of F-actin) was performed on 15 cells using the OrientationJ plugin of the ImageJ 1.47 software.” |
| 120 | 2021 | Moore et al. (2021) Actin cables and comet tails organize mitochondrial networks in mitosis Nature · doi:10.1038/s41586-021-03309-5 | actin cytoskeleton and mitochondrial networks | Color-coded orientation map | “Orientation maps of the segmented cables were generated in the Fiji plugin OrientationJ, using a cubic spline gradient with gaussian window sigma = 2 pix.” |
| 121 | 2021 | Myram et al. (2021) A Multitubular Kidney-on-Chip to Decipher Pathophysiological Mechanisms in Renal Cystic Diseases Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2021.624553 | actin cytoskeleton in kidney tubules | Distribution (directionality histogram) | “Distribution of F-actin local orientation as assessed by OrientationJ software for PCT Pkd1 +/- (blue) and Pkd1 -/- (red) cells.” |
| 122 | 2021 | Girardi et al. (2021) TGFβ signaling curbs cell fusion and muscle regeneration Nature Communications · doi:10.1038/s41467-020-20289-8 | actin cytoskeleton, muscle regeneration | Color-coded orientation map | “These pictures were analyzed with OrientationJ (ImageJ Plug-in) to obtain a color-coded orientation mask.” |
| 123 | 2021 | Jin et al. (2021) Emergent Differential Organization of Airway Smooth Muscle Cells on Concave and Convex Tubular Surface Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.717771 | airway smooth muscle tissue engineering | Distribution (directionality histogram) | “Assessment of Cell Orientation Quantification of ASMC orientation cultured on the concave and convex surfaces and the cylinder axis was performed using the distribution analysis function in the plugin OrientationJ” |
| 124 | 2021 | Samandari et al. (2021) A simple, low cost and reusable microfluidic gradient strategy and its application in modeling cancer invasion Scientific Reports · doi:10.1038/s41598-021-89635-0 | cancer cell invasion in microfluidics | Color-coded orientation map | “the color maps were generated using the "OrientationJ" plugin in ImageJ” |
| 125 | 2021 | Sharifi et al. (2021) An exploratory assessment of stretch-induced transmural myocardial fiber kinematics in right ventricular pressure overload Scientific Reports · doi:10.1038/s41598-021-83154-8 | cardiac myocardial fiber kinematics | orientation/coherency analysis | “Image processing and fiber orientation analysis of histological sections were performed using the OrientationJ toolbox in ImageJ” |
| 126 | 2021 | Cavinato et al. (2021) Progressive Microstructural Deterioration Dictates Evolving Biomechanical Dysfunction in the Marfan Aorta Frontiers in Cardiovascular Medicine · doi:10.3389/fcvm.2021.800730 | cardiac tissue, aortic microstructure | Distribution (directionality histogram) | “the in-plane primary orientation and alignment were estimated via a distribution of orientations for each circumferential-axial section” |
| 127 | 2021 | Jannasch et al. (2021) Optical coherence tomography and multiphoton microscopy offer new options for the quantification of fibrotic aortic valve disease in ApoE-/- mice Scientific Reports · doi:10.1038/s41598-021-85142-4 | cardiac valve fibrosis | Coherency map | “The degree of organization of collagen fibers was retrieved using the plugin OrientationJ for ImageJ.” |
| 128 | 2021 | Wu et al. (2021) High Resolution and Labeling Free Studying the 3D Microstructure of the Pars Tensa-Annulus Unit of Mice Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.720383 | collagen fiber alignment in ear tissue | Orientation and Coherency analysis | “OrientationJ in ImageJ was used to quantify the orientation and coherency features of the collagen fibers constituting the pars tensa across the thickness” |
| 129 | 2021 | Jones et al. (2021) Pten regulates collagen fibrillogenesis by fibroblasts through SPARC PLOS ONE · doi:10.1371/journal.pone.0245653 | collagen/ECM fibrillogenesis | Measure | “fiber orientation was quantified using the ImageJ plugin OrientationJ [ 25 ] with previously published settings [ 24 ]” |
| 130 | 2021 | Stocco et al. (2021) Age-Dependent Remodeling in Infrapatellar Fat Pad Adipocytes and Extracellular Matrix: A Comparative Study Frontiers in Medicine · doi:10.3389/fmed.2021.661403 | collagen/ECM in adipose tissue | Color-coded orientation map | “OrientationJ is a Java plugin for ImageJ/FIJI which allows to visualize with a Hue, Saturation and Brightness (HSB) map the directionality within the sample.” |
| 131 | 2021 | Drain et al. (2021) Matrix compliance permits NF-κB activation to drive therapy resistance in breast cancer Journal of Experimental Medicine · doi:10.1084/jem.20191360 | collagen/ECM in tumors | Dominant Direction + Coherency | “Fiber coherency was measured in the dominant fiber direction as determined by OrientationJ for each image.” |
| 132 | 2021 | Budden et al. (2021) Ultraviolet light-induced collagen degradation inhibits melanoma invasion Nature Communications · doi:10.1038/s41467-021-22953-z | collagen/ECM in tumors | orientation/coherency analysis | “Fibre orientation analysis was performed using ImageJ OrientationJ plugin” |
| 133 | 2021 | Parvanian et al. (2021) Exosomal Vimentin from Adipocyte Progenitors Protects Fibroblasts against Osmotic Stress and Inhibits Apoptosis to Enhance Wound Healing International Journal of Molecular Sciences · doi:10.3390/ijms22094678 | collagen/ECM in wound healing | Color-coded orientation map | “Color maps of the collagen I fibers generated using the OrientationJ plugin.” |
| 134 | 2021 | Silvani et al. (2021) Biomechanical Characterization of Endothelial Cells Exposed to Shear Stress Using Acoustic Force Spectroscopy Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2021.612151 | endothelial cell cytoskeleton alignment | Distribution (directionality histogram) | “Distribution of EC orientations after 4 h (green), 24h (red), and 48 h (blue) from seeding obtained with "orientationJ distribution" of ImageJ software.” |
| 135 | 2021 | Garrison et al. (2021) Fibronectin fibril alignment is established upon initiation of extracellular matrix assembly Molecular Biology of the Cell · doi:10.1091/mbc.e20-08-0533 | fibronectin ECM assembly, fibroblast mechanobiology | Color-coded orientation map, Distribution (directionality histogram), Dominant Direction | “individual matrix assembly site orientations were calculated for individual cells using OrientationJ, averaged across cells (WI-38 n = 27, NIH 3T3 n = 36), and plotted from –90° to 90°.” |
| 136 | 2021 | Tagliaferri et al. (2021) Aqueous Inks of Pristine Graphene for 3D Printed Microsupercapacitors with High Capacitance ACS Nano · doi:10.1021/acsnano.1c06535 | materials/nanofibers | structure tensor (orientation/coherency analysis) | “The platelet orientation angle was quantified calculating the gradient structure tensor of the tomographic images (via the OrientationJ plug-in for ImageJ)” |
| 137 | 2021 | Belousov et al. (2021) Thermochemical Laser-Induced Periodic Surface Structures Formation by Femtosecond Laser on Hf Thin Films in Air and Vacuum Materials · doi:10.3390/ma14216714 | materials/nanofibers | Distribution (directionality histogram) + Color-coded orientation map | “The analysis of SEM images in the ImageJ program using the OrientationJ plugin was performed in the Orientation Distribution module with the Gaussian Gradient structural tensor.” |
| 138 | 2021 | Memarian et al. (2021) Active nematic order and dynamic lane formation of microtubules driven by membrane-bound diffusing motors Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2117107118 | microtubule cytoskeleton dynamics | Distribution (directionality histogram) | “ImageJ plugin OrientationJ to calculate angular distributions of MTs with a bin size of 5° to calculate angular distributions of the MTs using the published method from Inoue et al.” |
| 139 | 2021 | Hsieh et al. (2021) Detection of endophenotypes associated with neuropsychiatric deficiencies in a mouse model of tuberous sclerosis complex using diffusion tensor imaging Brain Pathology · doi:10.1111/bpa.12870 | myelination complexity in neuropsychiatric tissue | Coherency map / Measure | “Quantitative coherency analysis using OrientationJ to assess the myelination complexity in the ACC and the hippocampal regions.” |
| 140 | 2021 | Osorio-Londoño et al. (2021) Pyrrole Plasma Polymer-Coated Electrospun Scaffolds for Neural Tissue Engineering Polymers · doi:10.3390/polym13223876 | neural tissue engineering scaffolds | orientation/coherency analysis | “Cell morphology and orientation of cell structures analysis was conducted in ImageJ/Fiji (NIH, Bethesda, MD, USA), with the OrientationJ plugin” |
| 141 | 2021 | Antonova et al. (2021) ECM-Mimetic Nylon Nanofiber Scaffolds for Neurite Growth Guidance Nanomaterials · doi:10.3390/nano11020516 | neuronal alignment, nanofiber scaffolds | orientation/coherency analysis | “Fiber orientation was determined using the OrientationJ plugin and Directionality ImageJ software” |
| 142 | 2021 | Alexander et al. (2021) Nasal administration of mitochondria reverses chemotherapy-induced cognitive deficits Theranostics · doi:10.7150/thno.53474 | neuronal tissue and brain imaging | Coherency map | “Percent area and coherency were quantified using ImageJ with the OrientationJ plugin as described before” |
| 143 | 2021 | Tribble et al. (2021) Retinal Ganglion Cell Degeneration in a Rat Magnetic Bead Model of Ocular Hypertensive Glaucoma Translational Vision Science & Technology · doi:10.1167/tvst.10.1.21 | optic nerve gliosis / neuroinflammation | Coherency and fiber alignment (Measure) | “GFAP fiber alignment (to detect process remodeling typical of gliosis in the optic nerve) was measured using OrientationJ” |
| 144 | 2022 | Potolitsyna et al. (2022) Long non-coding RNA HOTAIR regulates cytoskeleton remodeling and lipid storage capacity during adipogenesis Scientific Reports · doi:10.1038/s41598-022-14296-6 | actin cytoskeleton | Coherency map | “Actin cytoskeleton coherence was measured from phalloidin staining with the OrientationJ plugin” |
| 145 | 2022 | Knox et al. (2022) Microbial-derived metabolites induce actin cytoskeletal rearrangement and protect blood-brain barrier function iScience · doi:10.1016/j.isci.2022.105648 | actin cytoskeleton | Coherency map | “The coherence of the actin filamentous directionality was measured using OrientationJ, a plugin for Fiji/ImageJ, with the region of interest (ROI) set to the entirety of each im…” |
| 146 | 2022 | Tsai et al. (2022) Activated I-BAR IRSp53 clustering controls the formation of VASP-actin-based membrane protrusions Science Advances · doi:10.1126/sciadv.abp8677 | actin cytoskeleton | orientation/coherency analysis | “we performed image analysis using the "OrientationJ" plugin in ImageJ/Fiji” |
| 147 | 2022 | Kato et al. (2022) Mucus concentration-dependent biophysical abnormalities unify submucosal gland and superficial airway dysfunction in cystic fibrosis Science Advances · doi:10.1126/sciadv.abm9718 | airway mucus and mucins | Color-coded orientation map | “Inset was falsely colored according to angular alignment of pixels quantified with OrientationJ.” |
| 148 | 2022 | Casarin et al. (2022) Porcine Small Intestinal Submucosa (SIS) as a Suitable Scaffold for the Creation of a Tissue-Engineered Urinary Conduit: Decellularization, Biomechanical and Biocompatibility Characterization Using New Approaches International Journal of Molecular Sciences · doi:10.3390/ijms23052826 | biomaterial scaffold characterization | Coherency map | “the coherency (C) parameter, to estimate the local orientation of the fibres (values around 0 indicate isotropic areas, whereas values around 1 indicate highly orien…” |
| 149 | 2022 | Todesco et al. (2022) A New Detergent for the Effective Decellularization of Bovine and Porcine Pericardia Biomimetics · doi:10.3390/biomimetics7030104 | cardiac tissue engineering | Coherency map | “Coherency (C) was calculated for collagen and elastin to check the local dominant fiber orientation in the Z-stack images using OrientationJ, an ImageJ plugin” |
| 150 | 2022 | Kim et al. (2022) Pocket CLARITY enables distortion-mitigated cardiac microstructural tissue characterization of large-scale specimens Frontiers in Cardiovascular Medicine · doi:10.3389/fcvm.2022.1037500 | cardiac tissue microstructure | Dominant Direction | “Fiber orientation was calculated using the OrientationJ ( 33 ) plugin for Fiji at 10 × 10 pixel blocks based on structure tensor analysis.” |
| 151 | 2022 | Palmosi et al. (2022) Small intestinal submucosa-derived extracellular matrix as a heterotopic scaffold for cardiovascular applications Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2022.1042434 | cardiovascular tissue engineering, extracellular matrix | Coherency map | “The coherence of collagen fibers was calculated to verify the dominant local orientation of the images using OrientationJ” |
| 152 | 2022 | Tavakoli et al. (2022) Developing Novel Fabrication and Optimisation Strategies on Aggregation-Induced Emission Nanoprobe/Polyvinyl Alcohol Hydrogels for Bio-Applications Molecules · doi:10.3390/molecules27031002 | cell alignment in hydrogel scaffolds | Measure | “OrientationJ plugin was used to measure the orientation of cells in the input binary (8-bit) microscope images.” |
| 153 | 2022 | Kim et al. (2022) Anterior cruciate ligament microfatigue damage detected by collagen autofluorescence in situ Journal of Experimental Orthopaedics · doi:10.1186/s40634-022-00507-6 | collagen/ECM in ligament tissue | Distribution (directionality histogram), Coherency parameter, Color-coded orientation map | “The output from the OrientationJ analysis, in terms of distribution and dominant direction, was the histogram of orientation angles, a coherency parameter and a color-coded map of fiber orientations.” |
| 154 | 2022 | Alfonso et al. (2022) Comprehensive Profiling of Early Neoplastic Gastric Microenvironment Modifications and Biodynamics in Impaired BMP-Signaling FoxL1+-Telocytes Biomedicines · doi:10.3390/biomedicines11010019 | collagen/ECM in tumors | Distribution (directionality histogram) | “Analysis using the OrientationJ plugin in ImageJ indicates a similar distribution of fiber angles between the control and BmpR1a △FoxL1+ mice in the middle part of the glands” |
| 155 | 2022 | Jenkins et al. (2022) Age alters the oncogenic trajectory toward luminal mammary tumors that activate unfolded proteins responses Aging Cell · doi:10.1111/acel.13665 | collagen/ECM in tumors | orientation/coherency analysis | “SHG images were then analyzed using OrientationJ in ImageJ” |
| 156 | 2022 | Koorman et al. (2022) Spatial collagen stiffening promotes collective breast cancer cell invasion by reinforcing extracellular matrix alignment Oncogene · doi:10.1038/s41388-022-02258-1 | collagen/ECM in tumors | Distribution (directionality histogram) | “Collagen alignment (collagen bundle angle variability perpendicular to the organoid) by collectively invading H7 organoids was visualized using confocal reflection microscopy (insets) ( C ) and quantified using OrientationJ in ( D ).” |
| 157 | 2022 | Capparelli et al. (2022) Targeting SOX10-deficient cells to reduce the dormant-invasive phenotype state in melanoma Nature Communications · doi:10.1038/s41467-022-28801-y | collagen/ECM in tumors | orientation/coherency analysis | “Using FIJI's plugin OrientationJ, a comprehensive orientation analysis was conducted using similar plugin settings for all the images evaluated.” |
| 158 | 2022 | Bonanini et al. (2022) In vitro grafting of hepatic spheroids and organoids on a microfluidic vascular bed Angiogenesis · doi:10.1007/s10456-022-09842-9 | hepatic tissue engineering, microvessel orientation | Measure | “Maximum intensity projections from each chip were used to calculate the average microvessel orientation and microvessel area using the 'orientationJ analysis' tool” |
| 159 | 2022 | Whyte et al. (2022) Dynamic actuation enhances transport and extends therapeutic lifespan in an implantable drug delivery platform Nature Communications · doi:10.1038/s41467-022-32147-w | implantable drug delivery platform | Coherency map | “Using the OrientationJ 2.0.5 plugin, the coherency of each ROI was calculated.” |
| 160 | 2022 | Shiota et al. (2022) C9orf72-Derived Proline:Arginine Poly-Dipeptides Modulate Cytoskeleton and Mechanical Stress Response Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.750829 | intermediate filament cytoskeleton | Distribution (directionality histogram) | “The bundle alignments of IFs were measured by the dispersion of the IF angles in whole cells using the OrientationJ plugin” |
| 161 | 2022 | Lintz et al. (2022) The degenerative impact of hyperglycemia on the structure and mechanics of developing murine intervertebral discs JOR SPINE · doi:10.1002/jsp2.1191 | intervertebral disc fibrous tissue | Dominant Direction | “Fiber orientation in the AF region was determined for wild type and diabetic samples using the OrientationJ plugin.” |
| 162 | 2022 | Liu et al. (2022) Magnetically assisted drop-on-demand 3D printing of microstructured multimaterial composites Nature Communications · doi:10.1038/s41467-022-32792-1 | materials/composite microstructure | Color-coded orientation map | “The image is colour-coded based on the microplatelet alignment using OrientationJ.” |
| 163 | 2022 | Orlov et al. (2022) Fluid Handling Dynamics and Durability of Silver-Containing Gelling Fiber Dressings Tested in a Robotic Wound System Advances in Skin & Wound Care · doi:10.1097/01.asw.0000823972.16446.ff | materials/nanofibers | Distribution (directionality histogram) | “OrientationJ" of the ImageJ software suite (version 1.X), which segments the fibers in the digital micrographs and calculates the probability function for their planar orientation” |
| 164 | 2022 | Kratzer et al. (2022) Vascularization of Poly-ε-Caprolactone-Collagen I-Nanofibers with or without Sacrificial Fibers in the Neurotized Arteriovenous Loop Model Cells · doi:10.3390/cells11233774 | materials/nanofibers | orientation/coherency analysis | “fiber orientation was defined using the ImageJ plugin OrientationJ” |
| 165 | 2022 | Otani et al. (2022) Meniscus surface texture is associated with degenerative changes in biological and biomechanical properties Scientific Reports · doi:10.1038/s41598-022-16206-2 | meniscus collagen/cartilage ECM | Dominant Direction | “The FIJI plug-in OrientationJ was used to evaluate collagen orientation.” |
| 166 | 2022 | Katti et al. (2022) Identification of evolutionarily conserved regulators of muscle mitochondrial network organization Nature Communications · doi:10.1038/s41467-022-34445-9 | muscle mitochondrial network organization | Distribution (directionality histogram) | “The images were then binarized and the OrientationJ Distributions plugin was used to determine the angles of the mitochondrial network.” |
| 167 | 2022 | Mao et al. (2022) Tension-driven multi-scale self-organisation in human iPSC-derived muscle fibers eLife · doi:10.7554/elife.76649 | muscle myofibrils / iPSC-derived muscle | Color-coded orientation map & Vector Field | “Vector field analysis of myofiber bundles was performed using the OrientationJ plugin ( Rezakhaniha et al., 2012 ) in Fiji ( Schindelin et al., 2012 ) combined with custom R scripts.” |
| 168 | 2022 | Brocca et al. (2022) Normal Cortical Myelination in Galectin-4-Deficient Mice Cells · doi:10.3390/cells11213485 | myelinated fiber alignment in cortex | Distribution (directionality histogram) and Measure (coherency) | “Distribution function of the OrientationJ plugin was used to build a weighted orientation histogram for each ROI” |
| 169 | 2022 | Stracuzzi et al. (2022) Risky interpretations across the length scales: continuum vs. discrete models for soft tissue mechanobiology Biomechanics and Modeling in Mechanobiology · doi:10.1007/s10237-021-01543-4 | soft tissue mechanobiology | orientation/coherency analysis | “such as the 'Directionality' tool or the 'OrientationJ' plugin in ImageJ” |
| 170 | 2022 | Thiagarajan et al. (2022) Pulsations and flows in tissues as two collective dynamics with simple cellular rules iScience · doi:10.1016/j.isci.2022.105053 | tissue dynamics and cellular flows | orientation/coherency analysis | “(2012) https://imagej.net/software/fiji/ OrientationJ plugin, Fiji Püspöki et al.” |
| 171 | 2022 | Janvier et al. (2022) Multimodal analysis of the differential effects of cyclic strain on collagen isoform composition, fibril architecture and biomechanics of tissue engineered tendon Journal of Tissue Engineering · doi:10.1177/20417314221130486 | tissue engineered tendon, collagen fibril alignment | Color-coded orientation map | “The ImageJ plug-in (OrientationJ) was used to visualise and quantify fibril orientation parallel to the strain axis (0° = parallel, shown as vertical in these images)” |
| 172 | 2022 | Maghin et al. (2022) Customized bioreactor enables the production of 3D diaphragmatic constructs influencing matrix remodeling and fibroblast overgrowth npj Regenerative Medicine · doi:10.1038/s41536-022-00222-x | tissue engineering, collagen/ECM | Coherency map | “Collagen coherency was calculated from SHG to verify the local dominant orientation of the fibers using OrientationJ, an ImageJ plugin” |
| 173 | 2022 | Fu et al. (2022) Adaptive structural changes in the motor cortex and white matter in Parkinson's disease Acta Neuropathologica · doi:10.1007/s00401-022-02488-3 | white matter axonal alignment | Coherency map | “The anisotropic properties of axons were characterised by their directional coherency coefficient, which was calculated by the 'OrientationJ' Java plugin for the ImageJ/Fiji software” |
| 174 | 2023 | Cesaria et al. (2023) Mutant-Dependent Local Orientational Correlation in Biofilms of Vibrio campbellii Revealed through Digital Processing of Light Microscopy Images International Journal of Molecular Sciences · doi:10.3390/ijms24065423 | Vibrio campbellii biofilm morphology | Coherency map, Orientation map, Measure | “the measured images were processed with OrientationJ to obtain orientation and coherency maps over the whole image extension.” |
| 175 | 2023 | Gudde et al. (2023) Vaginal Fibroblast Behavior as a Function of Stiffness Changes in a Polyisocyanide Hydrogel for Prolapse Repair ACS Applied Bio Materials · doi:10.1021/acsabm.3c00433 | actin cytoskeleton | Distribution (directionality histogram) | “distribution of the actin filament orientation on day 21 (ImageJ version 1.53c, plugin OrientationJ)” |
| 176 | 2023 | Liu et al. (2023) Endothelial discoidin domain receptor 1 senses flow to modulate YAP activation Nature Communications · doi:10.1038/s41467-023-42341-z | actin cytoskeleton | Orientation/coherency analysis | “we employed the OrientationJ plugin within the Fiji software to determine the orientation of actin filaments.” |
| 177 | 2023 | Tee et al. (2023) Actin polymerisation and crosslinking drive left-right asymmetry in single cell and cell collectives Nature Communications · doi:10.1038/s41467-023-35918-1 | actin cytoskeleton | Measure | “the angle of stress fibre tilt of each elliptical cell, single or in a time-lapse series, was measured using the OrientationJ Measure plugin” |
| 178 | 2023 | Castiglioni et al. (2023) Cluster-Assembled Zirconia Substrates Accelerate the Osteogenic Differentiation of Bone Marrow Mesenchymal Stem Cells Nanomaterials · doi:10.3390/nano13050801 | actin cytoskeleton | Orientation map | “Images derived from fluorescence microscopy for F-actin on bMSCs were analyzed using the OrientationJ plugin of ImageJ, as described in detail in [ 26 , 27 ], in order to compute an orientation map.” |
| 179 | 2023 | Angelini et al. (2023) A defective mechanosensing pathway affects fibroblast-to-myofibroblast transition in the old male mouse heart iScience · doi:10.1016/j.isci.2023.107283 | actin cytoskeleton, fibroblast mechanobiology | Color-coded orientation map | “Staining of F-actin shown in false color using the OrientationJ plugin (ImageJ algorithm) depicting the changes in cell polarization and actin fiber orientation” |
| 180 | 2023 | Krumbein et al. (2023) RNA binding protein IGF2BP2 expression is induced by stress in the heart and mediates dilated cardiomyopathy Communications Biology · doi:10.1038/s42003-023-05547-x | cardiac muscle myofibrils | Directionality analysis | “For the directionality of pixels in MF20 cardiomyocyte staining, ImageJ software was used, using the OrientationJ plugin” |
| 181 | 2023 | Casarin et al. (2023) Preliminary In Vitro Assessment of Decellularized Porcine Descending Aorta for Clinical Purposes Journal of Functional Biomaterials · doi:10.3390/jfb14030141 | cardiac tissue engineering | Coherency map | “collagen fibre distribution was evaluated through fast Fourier transform (FFT) and coherency (C) parameters, to determine the fibres' local orientation, using the plug-in OrientationJ” |
| 182 | 2023 | Korover et al. (2023) Functional defects in hiPSCs-derived cardiomyocytes from patients with a PLEKHM2-mutation associated with dilated cardiomyopathy and left ventricular non-compaction Biological Research · doi:10.1186/s40659-023-00442-5 | cardiac tissue engineering | Directionality (cell orientation analysis) | “the immunostained iPSCs derived CMs projections were transformed into binary images, and the transformed image was analyzed using OrientationJ for cell directionality.” |
| 183 | 2023 | Wang et al. (2023) 3D printing of mechanically functional meniscal tissue equivalents using high concentration extracellular matrix inks Materials Today Bio · doi:10.1016/j.mtbio.2023.100624 | cartilage tissue engineering | Color-coded orientation map | “OrientationJ plugin from Image J was used to create the color maps of the fiber orientation, while directionality plugin was used to quantify the mean orientation and angular dispersion of the collagen fibers” |
| 184 | 2023 | Barceló et al. (2023) Chondroitinase ABC Treatment Improves the Organization and Mechanics of 3D Bioprinted Meniscal Tissue ACS Biomaterials Science & Engineering · doi:10.1021/acsbiomaterials.3c00101 | cartilage/meniscal tissue engineering | Coherency map | “Analysis on the fiber orientation and coherency was carried out using the OrientationJ plugin in ImageJ software.” |
| 185 | 2023 | Chang et al. (2023) Multiparameter interferometric polarization-enhanced imaging differentiates carcinoma in situ from inflammation of the bladder: an ex vivo study Journal of Biomedical Optics · doi:10.1117/1.jbo.28.10.102907 | collagen/ECM in bladder carcinoma | Coherency map, Orientation angle distribution, Color-coded orientation map | “The local orientations of collagen fibers were quantified using OrientationJ (Version 2.0.5) with a 6-pixel ( ∼ 1.8 μ m ) Gaussian window structure tensor and color-coded on top of the SHG image” |
| 186 | 2023 | Hewitt et al. (2023) Lung extracellular matrix modulates KRT5+ basal cell activity in pulmonary fibrosis Nature Communications · doi:10.1038/s41467-023-41621-y | collagen/ECM in pulmonary fibrosis | Coherency map, Dominant Direction | “OrientationJ was used to measure fibre coherency utilising properties of the original image, so-called 'first-order statistics'.” |
| 187 | 2023 | Kasahara et al. (2023) Spatiotemporal single-cell tracking analysis in 3D tissues to reveal heterogeneous cellular response to mechanical stimuli Science Advances · doi:10.1126/sciadv.adf9917 | collagen/ECM in tissues | orientation/coherency analysis | “The orientation of collagen fibers was characterized by processing confocal images of collagen with OrientationJ ImageJ plugins” |
| 188 | 2023 | He et al. (2023) Extracellular matrix physical properties govern the diffusion of nanoparticles in tumor microenvironment Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2209260120 | collagen/ECM in tumors | Distribution (directionality histogram) | “The plugin OrientationJ-Distribution was applied to analyze the fiber orientation distribution automatically.” |
| 189 | 2023 | Raoux et al. (2023) Unveiling the lamellar structure of the human cornea over its full thickness using polarization-resolved SHG microscopy Light: Science & Applications · doi:10.1038/s41377-023-01224-0 | corneal collagen fibril organization | Coherency map; Dominant Direction | “We use the ImageJ plug-in OrientationJ, which is based on the local evaluation of the gradient structure tensor” |
| 190 | 2023 | Hedayati et al. (2023) Visualizing molecular deformation in fibrin networks under tensile loading via FLIM-FRET Chemical Communications · doi:10.1039/d3cc05281h | fibrin networks, biomaterial structure | Dominant Direction | “We used OrientationJ to estimate the local predominant orientation (see ESI † ).” |
| 191 | 2023 | Cetera et al. (2023) Region-specific reversal of epidermal planar polarity in the rosette fancy mouse Development · doi:10.1242/dev.202078 | hair follicle orientation, skin | Vector Field | “To determine the orientation of each hair follicle, the plug-in 'OrientationJ-Vector Field' was used” |
| 192 | 2023 | Basar et al. (2023) Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) Electrospun Nanofibers Containing Natural Deep Eutectic Solvents Exhibiting a 3D Rugose Morphology and Charge Retention Properties ACS Omega · doi:10.1021/acsomega.2c05838 | materials/nanofibers | orientation/coherency analysis | “Fiber orientation was analyzed using the OrientationJ plugin to the ImageJ (NIH) software.” |
| 193 | 2023 | Park et al. (2023) Engineered kirigami design of PVDF-Pt core-shell nanofiber network for flexible transparent electrode Scientific Reports · doi:10.1038/s41598-023-29812-5 | materials/nanofibers | orientation/coherency analysis | “OrientationJ, which is an ImageJ plug-in, was used to statistically analyze the orientation of PVDF nanofibers.” |
| 194 | 2023 | Taborda et al. (2023) Micropatterned Nanofiber Scaffolds of Salmon Gelatin, Chitosan, and Poly(vinyl alcohol) for Muscle Tissue Engineering ACS Omega · doi:10.1021/acsomega.3c06436 | materials/nanofibers | Distribution (directionality histogram) | “the SEM images were analyzed with ImageJ Software (NIH, version 1.50i, Bethesda, MD, USA) with the DiameterJ and OrientationJ plugins” |
| 195 | 2023 | Cai et al. (2023) Myogenic differentiation of human myoblasts and Mesenchymal stromal cells under GDF11 on NPoly-ɛ-caprolactone-collagen I-Polyethylene-nanofibers BMC Molecular and Cell Biology · doi:10.1186/s12860-023-00478-1 | materials/nanofibers | orientation/coherency analysis | “Fiber orientation was analyzed using the OrientationJ plugin (ImageJ) on 5 different images of the scaffolds taken in 10,000x magnification.” |
| 196 | 2023 | Lasenko et al. (2023) The Mechanical Properties of Nanocomposites Reinforced with PA6 Electrospun Nanofibers Polymers · doi:10.3390/polym15030673 | materials/nanofibers | Dominant Direction | “The fiber orientation was obtained using the ImageJ software's OrientationJ plug-in [ 43 , 44 ] (ImageJ, National Institutes of Health, Bethesda, MD, USA).” |
| 197 | 2023 | Maan et al. (2023) Multivalent interactions facilitate motor-dependent protein accumulation at growing microtubule plus-ends Nature Cell Biology · doi:10.1038/s41556-022-01037-0 | microtubule dynamics | Measure | “Each data point represents the average speed on one microtubule estimated using the imageJ plugin orientationJ.” |
| 198 | 2023 | Bao et al. (2023) A clustering-based method for estimating pennation angle from B-mode ultrasound images Wearable Technologies · doi:10.1017/wtc.2022.30 | muscle architecture in ultrasound | Distribution (directionality histogram) | “The DistributionJ within the OrientationJ plug-in was then utilized to create a table with the distribution of the orientation angle of the targeted aponeurosis and muscle fascicle.” |
| 199 | 2023 | Peters et al. (2023) Self-organizing behaviors of cardiovascular cells on synthetic nanofiber scaffolds APL Bioengineering · doi:10.1063/5.0172423 | nanofiber scaffold alignment, cardiovascular tissue engineering | Distribution (directionality histogram), Color-coded orientation map, Horizontal Alignment | “Each image was processed in ImageJ using OrientationJ's Distribution analysis function which outputs a distribution of angular occurrences from −90° to 90°.” |
| 200 | 2023 | Stocco et al. (2023) Development and preclinical evaluation of bioactive nerve conduits for peripheral nerve regeneration: A comparative study Materials Today Bio · doi:10.1016/j.mtbio.2023.100761 | nerve conduit fibers, peripheral nerve regeneration | Coherency | “organization/distribution of the fibers was also investigated determining the Coherency (C) by FFT [ 38 ] and OrientationJ [ 39 ]” |
| 201 | 2023 | Nakazawa et al. (2023) A human septin octamer complex sensitive to membrane curvature drives membrane deformation with a specific mesh-like organization Journal of Cell Science · doi:10.1242/jcs.260813 | septin cytoskeleton organization | Color-coded orientation map | “The ImageJ plugin OrientationJ displayed the orientation of the filaments on probability maps by color, and a spectrum displayed the angle distribution.” |
| 202 | 2023 | Rinoldi et al. (2023) Mesoporous Particle Embedded Nanofibrous Scaffolds Sustain Biological Factors for Tendon Tissue Engineering ACS Materials Au · doi:10.1021/acsmaterialsau.3c00012 | tendon tissue engineering | Measure | “Cell orientation was quantified based on confocal images using ImageJ (National Institute of Health, USA) by measuring cell cytoskeletons orientation (ImageJ software, OrientationJ).” |
| 203 | 2023 | Stocco et al. (2023) Development and In Vitro/In Vivo Comparative Characterization of Cryopreserved and Decellularized Tracheal Grafts Cells · doi:10.3390/cells12060888 | tracheal tissue engineering, decellularized grafts | Coherency | “Coherency (C) was determined to assess the local dominant orientation of collagen fibers; to achieve that, it was used the ImageJ plugin OrientationJ” |
| 204 | 2023 | Holroyd et al. (2023) Quantitative Image Processing for Three-Dimensional Episcopic Images of Biological Structures: Current State and Future Directions Biomedicines · doi:10.3390/biomedicines11030909 | white matter tissue | orientation/coherency analysis | “Similar methods were used to quantify white matter orientation by Walsh et al. [ 2 ], in this case employing the OrientationJ plugin of ImageJ.” |
| 205 | 2024 | Ray et al. (2024) Confinement promotes nematic alignment of spindle-shaped cells during Drosophila embryogenesis Development · doi:10.1242/dev.202577 | Drosophila embryo cell alignment | Vector Field | “Vector fields were obtained with the OrientationJ plugin (local window of 4 pixels for DE-cad, local window of 6 pixels for MTs, and grid size of 10 vectors” |
| 206 | 2024 | Maxey et al. (2024) Contractile responses of engineered human μmyometrium to prostaglandins and inflammatory cytokines APL Bioengineering · doi:10.1063/5.0233737 | actin cytoskeleton | Coherency map | “Cytoskeletal alignment was calculated using actin signal and ImageJ OrientationJ.” |
| 207 | 2024 | Jühlen et al. (2024) Alteration of actin cytoskeletal organisation in fetal akinesia deformation sequence Scientific Reports · doi:10.1038/s41598-023-50615-1 | actin cytoskeleton | orientation/coherency analysis | “actin and focal adhesion orientation was investigated in ImageJ using plugins Analyze Skeleton (2D/3D; version 3.3.0) and OrientationJ Analysis (version 2.0.4), respectively” |
| 208 | 2024 | Sakamoto et al. (2024) Composite branched and linear F-actin maximize myosin-induced membrane shape changes in a biomimetic cell model Communications Biology · doi:10.1038/s42003-024-06528-4 | actin cytoskeleton | structure-tensor order parameter | “We measure the orientation field of F-actin using a public domain program OrientationJ implemented as a Fiji/ImageJ plugin.” |
| 209 | 2024 | Sakamoto et al. (2024) Mechanical power is maximized during contractile ring-like formation in a biomimetic dividing cell model Nature Communications · doi:10.1038/s41467-024-53228-y | actin cytoskeleton | orientation field measurement / Coherency map | “We measure the orientation field of F-actin using a public domain program OrientationJ implemented as a Fiji/ImageJ plugin.” |
| 210 | 2024 | Popęda et al. (2024) Emerin mislocalization during chromatin bridge resolution can drive prostate cancer cell invasiveness in a collagen-rich microenvironment Experimental & Molecular Medicine · doi:10.1038/s12276-024-01308-w | actin cytoskeleton in cancer cells | Coherency map | “F-actin coherency was calculated from the projected confocal images using the Orientation J plugin ( http://bigwww.epfl.ch/demo/orientationj/ ) for ImageJ 32 , with the F-actin fiber coherency parameter calculated for selected cells.” |
| 211 | 2024 | Ma et al. (2024) Melt Electrowriting Combined with Fused Deposition Modeling Printing for the Fabrication of Three-Dimensional Biomimetic Scaffolds for Osteotendinous Junction Regeneration International Journal of Nanomedicine · doi:10.2147/ijn.s449952 | biomimetic scaffolds / tissue engineering | Color-coded orientation map | “The OrientationJ plug-in for ImageJ was employed to color-code fibers based on their orientation, as shown in Figure 2I and J.” |
| 212 | 2024 | Muñoz et al. (2024) FiberO for an automated quantitative analysis of fibers orientation and organization in biological fibrous tissues Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2024.1497837 | bone and biological fibrous tissues | Color-coded orientation map | “OrientationJ computes the orientations based on the gradient structure tensor in a local neighborhood ( Püspöki et al., 2016 ).” |
| 213 | 2024 | Castanheira et al. (2024) In-Bath 3D Printing of Anisotropic Shape-Memory Cryogels Functionalized with Bone-Bioactive Nanoparticles ACS Applied Materials & Interfaces · doi:10.1021/acsami.3c18290 | bone/mineralized tissue cryogels | orientation/coherency analysis | “The analysis of the pore orientation was performed resorting to OrientationJ plugin from ImageJ.” |
| 214 | 2024 | Prondzynski et al. (2024) Efficient and reproducible generation of human iPSC-derived cardiomyocytes and cardiac organoids in stirred suspension systems Nature Communications · doi:10.1038/s41467-024-50224-0 | cardiac tissue engineering | structure-tensor order parameter | “utilizes ImageJ Plugins (OrientationJ) and a custom-made Matlab script for structural analysis of the cells Resulting parameters for sarcomere alignment referred to as "Orientational Order Parameter" (OOP)” |
| 215 | 2024 | Fang et al. (2024) Collagen denaturation in post-run Achilles tendons and Achilles tendinopathy: In vivo mechanophysiology and magnetic resonance imaging Science Advances · doi:10.1126/sciadv.ado2015 | collagen fiber alignment in tendons | orientation/coherency analysis | “The disrupted fiber orientation in SHG images was quantitatively analyzed using the "OrientationJ" plug-in of the ImageJ software” |
| 216 | 2024 | Lenzi et al. (2024) Alterations in the Structure, Composition, and Organization of Galactosaminoglycan-Containing Proteoglycans and Collagen Correspond to the Progressive Stages of Dupuytren's Disease International Journal of Molecular Sciences · doi:10.3390/ijms25137192 | collagen/ECM in Dupuytren's disease | Orientation analysis | “The orientation analysis of collagen structure was performed using the second harmonic generation of collagen fibers images (Z-series of confocal stacks) from control and DD patients built by OrientationJ plugin” |
| 217 | 2024 | Plesselova et al. (2024) Multicompartmentalized Microvascularized Tumor-on-a-Chip to Study Tumor-Stroma Interactions and Drug Resistance in Ovarian Cancer Cellular and Molecular Bioengineering · doi:10.1007/s12195-024-00817-y | collagen/ECM in tumors | Color-coded orientation map & Distribution (directionality histogram) | “the orientation of the collagen fibers was determined in ImageJ (FIJI) using the OrientationJ plugin for Hue, Saturation and Brightness (HSB) color-survey maps and OrientationJ distribution measurement.” |
| 218 | 2024 | Khalil et al. (2024) A YAP-centered mechanotransduction loop drives collective breast cancer cell invasion Nature Communications · doi:10.1038/s41467-024-49230-z | collagen/ECM in tumors | Coherency map | “OrientationJ determines the local orientation (from −90° up to 90°) and coherency (from 0 to 1) of every pixel relative to its neighbor in rectangular regions (30 × 50 μm) of the Collagen I” |
| 219 | 2024 | Roy et al. (2024) Implanting mechanically reprogrammed fibroblasts for aged tissue regeneration and wound healing Aging Cell · doi:10.1111/acel.14032 | collagen/ECM in wound healing | orientation/coherency analysis | “The fiber alignment of collagen I deposited by the implanted cells was computed by the OrientationJ Fiji plugins” |
| 220 | 2024 | Nejad et al. (2024) Stress-shape misalignment in confluent cell layers Nature Communications · doi:10.1038/s41467-024-47702-w | confluent cell layers | structure tensor (orientation & coherency) | “Cell orientations were determined using the ImageJ plugin OrientationJ.” |
| 221 | 2024 | Du et al. (2024) Myosin II mediates Shh signals to shape dental epithelia via control of cell adhesion and movement PLOS Genetics · doi:10.1371/journal.pgen.1011326 | dental epithelial tissue morphogenesis | Color-coded orientation map | “Analysis of nuclear orientations in 4 representative E13.5 control incisor germs using OrientationJ reveals cell alignment around the forming enamel knot” |
| 222 | 2024 | Forouharshad et al. (2024) Biomimetic electrospun PVDF/self-assembling peptide piezoelectric scaffolds for neural stem cell transplantation in neural tissue engineering RSC Advances · doi:10.1039/d4ra02309a | electrospun nanofiber scaffolds | Coherency | “fiber alignment was quantified as a coherency value by OrientationJ” |
| 223 | 2024 | Tai et al. (2024) The Effect of Aligned and Random Electrospun Fibers Derived from Porcine Decellularized ECM on Mesenchymal Stem Cell-Based Treatments for Spinal Cord Injury Bioengineering · doi:10.3390/bioengineering11080772 | electrospun nanofibers, tissue engineering | Measure | “DiameterJ and OrientationJ plugins were employed to measure the diameter and orientation of the fibers.” |
| 224 | 2024 | Kim et al. (2024) Long noncoding RNA MALAT1 mediates fibrous topography-driven pathologic calcification through trans-differentiation of myoblasts Materials Today Bio · doi:10.1016/j.mtbio.2024.101182 | fibrous biomaterial/scaffold orientation | Distribution (directionality histogram) | “PSF and PTFE direction of orientation was measured using OrientationJ Distribution plugin in the Fiji software.” |
| 225 | 2024 | Llopis-Grimalt et al. (2024) Nanostructured Implant-Tissue Interface Assessment Using a Three-Dimensional Gingival Tissue Equivalent ACS Omega · doi:10.1021/acsomega.4c02253 | gingival tissue engineering | orientation/coherency analysis | “they were analyzed using the FIJI software Plugin OrientationJ” |
| 226 | 2024 | Seo et al. (2024) Mechanical shutdown of battery separators: Silicon anode failure Nature Communications · doi:10.1038/s41467-024-54313-y | materials/battery separators | orientation/coherency analysis | “The structural information of the PE and HM separators, including the fiber thickness, orientation, and particle size, was gathered from their SEM images using ImageJ and OrientationJ software” |
| 227 | 2024 | Hackert et al. (2024) Inductive Heating of Ceramic Matrix Composites (CMC) for High-Temperature Applications Materials · doi:10.3390/ma17102175 | materials/ceramic composites | Distribution (directionality histogram) | “The fiber orientation was analyzed with imageJ [ 30 ] using the orientationJ plugin with its analysis and distribution functions.” |
| 228 | 2024 | Sousa et al. (2024) The Effect of Substrate Properties on Cellular Behavior and Nanoparticle Uptake in Human Fibroblasts and Epithelial Cells Nanomaterials · doi:10.3390/nano14040342 | materials/nanofibers | Measure | “ImageJ (National Institutes of Health, Bethesda, MD, USA) and the OrientationJ plugin were used to determine the average diameter and orientation of the fibers.” |
| 229 | 2024 | Pawar et al. (2024) 3D Melt Blowing of Elastollan Thermoplastic Polyurethane for Tissue Engineering Applications: A Pilot Study Manufacturing Letters · doi:10.1016/j.mfglet.2024.09.043 | materials/nanofibers | Coherency | “The OrientationJ plugin of ImageJ was used to determine the average fiber alignment, expressed as the degree of angular coherency (%), for each group using the 200X images” |
| 230 | 2024 | Gao et al. (2024) Myotube formation on micropatterns guiding by centripetal cellular motility and crowding Materials Today Bio · doi:10.1016/j.mtbio.2024.101195 | muscle myofibrils | orientation/coherency analysis | “we assessed myoblast alignment, a morphological indicator closely associated with the initiation of myotube formation, by quantifying stress fiber orientation using the OrientationJ plugin” |
| 231 | 2024 | Skillin et al. (2024) Stiffness anisotropy coordinates supracellular contractility driving long-range myotube-ECM alignment Science Advances · doi:10.1126/sciadv.adn0235 | muscle tissue engineering, myotube-ECM alignment | Vector Field | “Myotube alignment and nematic correlation length (ξ nn ) were quantified using OrientationJ and custom scripts” |
| 232 | 2024 | Comrie et al. (2024) Identification of diffusion, kurtosis, and propagator MRI markers of Alzheimer's disease pathology in post-mortem human tissue Imaging Neuroscience · doi:10.1162/imag_a_00164 | neuronal alignment in Alzheimer's pathology | Color-coded orientation map | “OrientationJ was applied using a structure tensor with a Gaussian window of 2 pixels and a cubic spline gradient algorithm where the hue corresponds to orientation, the color saturation corresponds to the fiber coherency” |
| 233 | 2024 | Bonaventura et al. (2024) Evaluating backscattering polarized light imaging microstructural mapping capabilities through neural tissue and analogous phantom imaging Journal of Biomedical Optics · doi:10.1117/1.jbo.29.5.052914 | neuronal tissue and polarized light imaging | Color-coded orientation map | “OrientationJ was applied using a structure tensor having a gaussian window of 2 pixels and a cubic spline gradient algorithm where the hue corresponds to orientation, the color saturation corresponds to the fiber coherency” |
| 234 | 2024 | Melogno et al. (2024) A transient radial cortical microtubule array primes cell division in Arabidopsis Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2320470121 | plant cell cortical microtubules | Vector Field | “we next analyzed CMT orientation with respect to the stem axis in NPA-treated plants, using the OrientationJ plugin in Fiji.” |
| 235 | 2024 | Reveley et al. (2024) Diffusion kurtosis imaging, MAP-MRI and NODDI selectively track gray matter myelin density in the primate cerebral cortex Imaging Neuroscience · doi:10.1162/imag_a_00368 | primate brain myelin density | structure tensor | “the structure tensor as implemented in the "OrientationJ" ImageJ package using a local Gaussian window σ = 85 pixels and image gradients computed with a cubic spline” |
| 236 | 2024 | Henze et al. (2024) Effect of epiretinal electrical stimulation on the glial cells in a rabbit retinal eyecup model Frontiers in Neuroscience · doi:10.3389/fnins.2024.1290829 | retinal glial cell alignment | Orientation and Coherency | “inner microglia in each circle were analyzed for orientation and coherency using the FIJI OrientationJ plug-in relative to the central lesion axis” |
| 237 | 2024 | Daly et al. (2024) Designer peptide-DNA cytoskeletons regulate the function of synthetic cells Nature Chemistry · doi:10.1038/s41557-024-01509-w | synthetic cells, peptide-DNA cytoskeleton | Distribution (directionality histogram) | “Alignment fraction analysis was performed using the OrientationJ Analysis plugin on ImageJ.” |
| 238 | 2025 | Elblová et al. (2025) Geometrically constrained cytoskeletal reorganisation modulates DNA nanostructures uptake Journal of Materials Chemistry B · doi:10.1039/d5tb00074b | actin cytoskeleton | orientation/coherency analysis | “Cytoskeleton filaments orientation analysis was performed using the ImageJ plugin "OrientationJ".” |
| 239 | 2025 | Dessalles et al. (2025) Interplay of actin nematodynamics and anisotropic tension controls endothelial mechanics Nature Physics · doi:10.1038/s41567-025-02847-3 | actin cytoskeleton | Dominant Direction | “Actin fibre orientation was obtained from the images of phalloidin stainings using the OrientationJ plug-in in ImageJ” |
| 240 | 2025 | Shimolina et al. (2025) Comparison of viscoelastic properties of breast cancer and normal cells using AFM, FLIM and ToF-SIMS techniques Scientific Reports · doi:10.1038/s41598-025-31162-3 | actin cytoskeleton | Vector Field | “The orientation of actin filaments in cells was analyzed using the structure tensor method via the ImageJ plugin OrientationJ (v2.0.7)” |
| 241 | 2025 | Tarantino et al. (2025) Revolutionizing radiotherapy: gold nanoparticles with polyphenol coating as novel enhancers in breast cancer cells-an in vitro study Discover Nano · doi:10.1186/s11671-025-04186-x | actin cytoskeleton | Coherency map | “Morphometric quantification (coherency of F-actin) was performed on 15 cells using the OrientationJ plugin of the ImageJ 1.53a software.” |
| 242 | 2025 | Valkov et al. (2025) Multilayer Ti-Cu Oxide Coatings on Ti6Al4V: Balancing Antibacterial Activity, Mechanical Strength, Corrosion Resistance, and Cytocompatibility Journal of Functional Biomaterials · doi:10.3390/jfb17010016 | actin cytoskeleton and osteoblast adhesion | Coherency map and Measure | “OrientationJ measure was then applied to each ROI to extract coherency values, which served as the primary quantitative metric of cytoskeletal alignment.” |
| 243 | 2025 | Eckert et al. (2025) Capturing nematic order on tissue surfaces of arbitrary geometry Nature Communications · doi:10.1038/s41467-025-62694-x | actin cytoskeleton on curved tissue surfaces | structure-tensor order parameter | “OrientationJ computes the largest eigendirection of the structure tensor for each pixel, i.e., its intensity orientation, of the image.” |
| 244 | 2025 | Hu et al. (2025) Piezo1-mediated mechanotransduction controls osteocyte maturation and dendrite development via a YAP-CCN-Src signaling axis Nature Communications · doi:10.1038/s41467-025-65636-9 | bone/mineralized tissue | Distribution (directionality histogram) | “dendrite orientation distribution was analyzed with the OrientationJ Plugin in Fiji” |
| 245 | 2025 | Jia et al. (2025) Integrated biomimetic bioprinting of perichondrium with cartilage for auricle reconstruction Bioactive Materials · doi:10.1016/j.bioactmat.2025.02.011 | cartilage tissue engineering | Coherency map, Color-coded orientation map | “OrientationJ, an ImageJ plugin developed in-house based on structure tensors [ 38 ].” |
| 246 | 2025 | Pahoff et al. (2025) Engineering biomimetic zonal properties in fibre-reinforced hydrogels for functional cartilage tissue engineering in vitro Materials Today Bio · doi:10.1016/j.mtbio.2025.102550 | cartilage tissue engineering, fibre alignment | orientation/coherency analysis | “each tomogram slice of the scanned constructs was analysed using OrientationJ in ImageJ software” |
| 247 | 2025 | Winkelbauer et al. (2025) Rapid Deep Vat Printing Using Photoclickable Collagen-Based Bioresins Advanced Healthcare Materials · doi:10.1002/adhm.202405105 | collagen bioresins, deep vat printing | Coherency map | “Alignment was quantified using the Fiji OrientationJ plugin (available at http://bigwww.epfl.ch/demo/orientationj ).” |
| 248 | 2025 | Gao et al. (2025) Multicellular force coordination constructs microchannel networks for barrier-free metastasis across extracellular matrix Science Advances · doi:10.1126/sciadv.adz4291 | collagen/ECM in tumors | Distribution (directionality histogram) | “Orientation distributions of collagen around intact single microchannels for each cell line (OrientationJ).” |
| 249 | 2025 | Sensi et al. (2025) Patient-derived extracellular matrix from decellularized high-grade serous ovarian carcinoma tissues as a biocompatible support for organoid growth Translational Oncology · doi:10.1016/j.tranon.2025.102523 | collagen/ECM in tumors | Coherency map | “Coherency (C) for collagen and elastin was quantified to evaluate the local prevailing orientation of the images, employing OrientationJ.” |
| 250 | 2025 | Olmedo-Moreno et al. (2025) Glioblastoma progression is hindered by melatonin-primed mesenchymal stromal cells through dynamic intracellular and extracellular reorganizations Theranostics · doi:10.7150/thno.104143 | collagen/ECM in tumors | Orientation analysis | “Orientation analysis of Sirius Red stained samples was performed with the ImageJ plugin OrientationJ.” |
| 251 | 2025 | Oak et al. (2025) Wnt signaling modulates mechanotransduction in the epidermis to drive hair follicle regeneration Science Advances · doi:10.1126/sciadv.adq0638 | collagen/actin alignment in epidermis | Coherency map; Measure | “the dominant orientation and coherency of the collagen network were calculated using OrientationJ” |
| 252 | 2025 | Huang et al. (2025) Tooth-on-a-chip to engineer early dental epithelial-mesenchymal interaction Materials Today Bio · doi:10.1016/j.mtbio.2025.102451 | dental epithelial-mesenchymal tissue engineering | Distribution (directionality histogram) | “The alignment angle distribution was simulated with the OrientationJ plugin in ImageJ (NIH, Bethesda, MD) normalized by Gaussian nonlinear regression.” |
| 253 | 2025 | Thompson et al. (2025) Multiple golgins are required to support extracellular matrix secretion, modification, and assembly Journal of Cell Biology · doi:10.1083/jcb.202411167 | extracellular matrix fiber alignment | Distribution (directionality histogram) | “Alignment is computed by the plug-in OrientationJ, which calculates the proportion of fibers within an image orientated in a similar direction.” |
| 254 | 2025 | Arafat et al. (2025) Fibre tracing in biomedical images: An objective comparison between seven algorithms PLOS ONE · doi:10.1371/journal.pone.0320006 | fibre tracing in biomedical images | Dominant Direction | “Twombli also incorporates OrientationJ to obtain the global alignment metric, determining the dominant direction of the fibrial structure.” |
| 255 | 2025 | Crestani et al. (2025) Loss of Fibronectin Fiber Tension in Glioblastoma is Associated with Microvascular Proliferations and Immune Cell Infiltration Advanced Science · doi:10.1002/advs.202416526 | fibronectin/ECM in glioblastoma | Dominant Direction | “The function "OrientationJ dominant direction" was then applied to each nucleus with a custom‐written macro and their distribution plotted in GraphPad Prism for visualization.” |
| 256 | 2025 | Tang et al. (2025) Development of Soy-Based Meat Analogues via Wet Twin-Screw Extrusion: Enhancing Textural and Structural Properties Through Whole Yeast Powder Supplementation Foods · doi:10.3390/foods14142479 | food materials / meat analogue texture | Distribution (directionality histogram) | “SEM images (×1500 magnification) were first converted to 8-bit grayscale and then analyzed using OrientationJ Distribution to extract the angular distribution of fiber orientation.” |
| 257 | 2025 | Carrera et al. (2025) Two-Dimensional Magnetic Orientation of Steel Fibers in Large Slab Elements Made of HPFRC Using an Industrial Robot Materials · doi:10.3390/ma19010125 | materials/fiber reinforced concrete | Distribution (directionality histogram) | “Image analysis was performed with FIJI ImageJ software (version 1.54) and the OrientationJ plugin (version 2.0.7) to objectively quantify orientation angles and distribution histograms.” |
| 258 | 2025 | Schlangen et al. (2025) Meat analogues: The relationship between mechanical anisotropy, macrostructure, and microstructure Current Research in Food Science · doi:10.1016/j.crfs.2025.100980 | meat analogues materials | Dominant Direction and Coherency | “The dominant direction in each image was determined and the coherency to this dominant direction was calculated with OrientationJ.” |
| 259 | 2025 | Liu et al. (2025) Filamented Light (FLight) Bioprinting of Mini-Muscles with Self-Renewal Potential Advanced Materials · doi:10.1002/adma.202501147 | muscle tissue engineering | Distribution (directionality histogram) | “Then the OrientationJ plugin was used to analyze the orientation distribution of the fibril structures.” |
| 260 | 2025 | Winkelbauer et al. (2025) Prolonged Cell Encapsulation and Gravity-independent Filamented Light Biofabrication of Muscle Constructs Advanced Science · doi:10.1002/advs.202512727 | muscle tissue engineering | Color-coded orientation map | “Confocal images of matured constructs were analyzed in Fiji (ImageJ) using the OrientationJ plugin” |
| 261 | 2025 | Huo et al. (2025) Myoblast Choreographic Alignment ACS Nano · doi:10.1021/acsnano.5c08392 | muscle tissue engineering; myoblast alignment | Vector Field; Color-coded orientation map | “The orientation director field and orientation colormap of the cell sheet were obtained using the ImageJ plugin OrientationJ, with both the window size and grid size set to 15 μm” |
| 262 | 2025 | Hoffmann et al. (2025) Optimizing the in vitro neuronal microenvironment to mitigate phototoxicity in live-cell imaging Stem Cell Research & Therapy · doi:10.1186/s13287-025-04591-0 | neuronal alignment and neurite directionality | orientation/coherency analysis | “The FIJI OrientationJ plugin developed by Fonck et al. in 2009 was here implemented in a novel region-based configuration to examine neurites emanating from each somata or somata cluster.” |
| 263 | 2025 | Liu et al. (2025) Filamented hydrogels as tunable conduits for guiding neurite outgrowth Materials Today Bio · doi:10.1016/j.mtbio.2025.101471 | neuronal alignment in hydrogels | Distribution (directionality histogram) | “the 'OrientationJ' plugin was used to evaluate the orientation and distribution of the aligned neurites” |
| 264 | 2025 | De et al. (2025) Mechanical Forces Guide Axon Growth through the Nigrostriatal Pathway in an Organotypic Model Advanced Science · doi:10.1002/advs.202500400 | neuronal axon growth and directionality | Measure | “Measures of directionality were obtained using the semi‐automated Fiji plugin OrientationJ, with default settings.” |
| 265 | 2025 | Karunakaran et al. (2025) The UNC5C T835M mutation associated with Alzheimer's disease leads to neurodegeneration involving oxidative stress and hippocampal atrophy in aged mice Molecular Neurodegeneration · doi:10.1186/s13024-025-00850-z | neuronal synaptic dendritic alignment | Distribution (directionality histogram) | “Maximum intensity projected 60 × images with PSD95 staining were analyzed using the OrientationJ plugin in ImageJ software by selecting the OrientationJ distribution” |
| 266 | 2025 | Long et al. (2025) Enhancing Tendon Regeneration: Investigating the Impact of Topography on the Secretome of Adipose-Derived Stem Cells Advanced Science · doi:10.1002/advs.202417447 | scaffold materials / tissue engineering | Color-coded orientation map | “OrientationJ" and "Directionality" plugins, from Fiji were used to create the color maps of the pore orientation and to generate data to plot the directionality curves” |
| 267 | 2025 | Pinon et al. (2025) An in vitro human vessel model to study Neisseria meningitidis colonization and vascular damages eLife · doi:10.7554/elife.107813 | vascular tissue, bacterial colonization | orientation/coherency analysis | “For each ROI, the mean fluorescence intensity has been subtracted from the background intensity (collagen matrix) and normalized by the mean of the non-infected areas' intensity” |
| 268 | 2025 | Wang et al. (2025) Neuroserpin normalization by mesenchymal stem cell therapy after encephalopathy of prematurity in neonatal rats Pediatric Research · doi:10.1038/s41390-024-03412-z | white matter microstructure, neuronal tissue | Measure | “Coherency of myelinated axons, as an inverse measure of complexity of white matter microstructure, was assessed using the "OrientationJ measure" function of ImageJ plugin OrientationJ” |
| 269 | 2026 | Jiang et al. (2026) Knockout of filamin A in KGN granulosa tumor cells impairs proliferation, cell cycle progression, migration, and cytoskeletal organization under mechanical stress Biological Research · doi:10.1186/s40659-026-00686-x | actin cytoskeleton | Distribution (directionality histogram) | “For in-depth orientation analysis and quantification of the distribution of phalloidin-stained filaments alignment between both cell types under each experimental condition, we used the software plugin tool OrientationJ (ImageJ/Fiji).” |
| 270 | 2026 | Chen et al. (2026) Stiff matrix-induced KRTAP2-3 expression suppresses ciliogenesis via actin tension-driven chromatin remodeling Cell Death & Disease · doi:10.1038/s41419-026-08678-1 | actin cytoskeleton | structure-tensor order parameter | “the alignment parameter (S), calculated by OrientationJ software, derived from the gradient structure tensor, was used to assess filaments alignment” |
| 271 | 2026 | Sarmiento-Jiménez et al. (2026) Role of the Glycine Transporter GlyT2 in the Neuronal Differentiation of PC12 Cells International Journal of Molecular Sciences · doi:10.3390/ijms27073026 | actin cytoskeleton | Coherency map | “F-actin bundle alignment was quantified using the OrientationJ plugin in Fiji 2.3” |
| 272 | 2026 | Mondal et al. (2026) F-actin organization excludes E-cadherin from the division furrow to ensure cytokinesis fidelity Life Science Alliance · doi:10.26508/lsa.202603664 | actin cytoskeleton | Distribution (directionality histogram) | “For each ROI, the filament orientation information was extracted using "OrientationJ (OJ) Distribution ( Rezakhaniha et al, 2012 )" plugin in Fiji.” |
| 273 | 2026 | Li et al. (2026) Biglycan Reconstitutes a Neonatal ECM Signaling Microenvironment to Drive Stem Cell-Mediated Tendon Regeneration via a Scaffold-Free Cell Sheet Platform International Journal of Molecular Sciences · doi:10.3390/ijms27104380 | actin cytoskeleton | Color-coded orientation map | “The orientation of the F-actin cytoskeleton was analyzed using the OrientationJ plugin 2.0.7 (Fiji/ImageJ 1.54p).” |
| 274 | 2026 | Garside et al. (2026) Single-Cell Morphomechanics of Prostate Cancer-Associated Fibroblasts Identifies Distinct Features Associated with Patient Outcome Advanced Science · doi:10.1002/advs.202522440 | actin cytoskeleton in cancer-associated fibroblasts | Distribution (directionality histogram) & Color-coded orientation map | “Angle distributions were calculated using the OrientationJ Distribution function with a local Gaussian window of σ = 2 pixels.” |
| 275 | 2026 | Kaivola et al. (2026) Restoring the tumour mechanophenotype of vocal fold cancer reverts its malignant properties Nature Materials · doi:10.1038/s41563-025-02473-7 | actin cytoskeleton in tumors | Coherency map | “Changes in the orientation (coherency) were assessed using the OrientationJ package in ImageJ software from MIPs of the confocal microscopy images (actin and β-catenin staining)” |
| 276 | 2026 | Franz et al. (2026) VE-Cadherin-Actin Regulation Promotes Mechanotransduction and Monolayer Maturation Involving a Tension-Sensitive Intermediate State Advanced Science · doi:10.1002/advs.202516423 | actin cytoskeleton, endothelial mechanotransduction | Coherency map + Dominant Direction | “Apparent coherency analysis of HUVECs exposed to different shear stress profiles was performed using the ImageJ 'OrientationJ' plugin and the 'Dominant Direction' tool based on phase contrast time‐lapse images.” |
| 277 | 2026 | Neuhäusler et al. (2026) Cell-instructive microfibers enable programmable alignment of bioprinted hMSC Bioactive Materials · doi:10.1016/j.bioactmat.2025.09.027 | bioprinted tissue engineering | orientation/coherency analysis | “The line diameter and fiber alignment were subsequently analyzed using fluorescence microscopy and the OrientationJ plugin (FIJI).” |
| 278 | 2026 | Melo et al. (2026) Metformin Downregulates the STAT Pathway and Reduces Bone Marrow Fibrosis in Primary Myelofibrosis Patients: Final Results of the Phase II FIBROMET Trial Hematological Oncology · doi:10.1002/hon.70163 | bone marrow fibrosis in myelofibrosis | Coherency map | “Fiber organization (coherency) and proximity (uniformity) were evaluated with the OrientationJ plugin using the same AOIs.” |
| 279 | 2026 | Lin et al. (2026) Spatiotemporal dynamics and regulation of suture morphology and collagen remodeling during trans-sutural distraction osteogenesis npj Regenerative Medicine · doi:10.1038/s41536-025-00448-5 | bone/mineralized tissue | Distribution (directionality histogram) | “the Riesz Filters method was utilized within the OrientationJ plugin for orientation analysis, and orientation distribution map” |
| 280 | 2026 | Zhao et al. (2026) Spatiotemporally programming the immune-osteogenic cascade with a dual-immunomodulatory scaffold for functional bone regeneration DOI pending | bone/mineralized tissue | Directionality (directionality histogram) | “The directionality of aligned collagen matrix and new bone matrix was analyzed using the "Directionality" and "OrientationJ" plugins in Fiji software.” |
| 281 | 2026 | Brown et al. (2026) Shear Stress Initiates Endothelial-to-Mesenchymal Transition in Endocardial Endothelial Cells Annals of Biomedical Engineering · doi:10.1007/s10439-026-03973-6 | cardiac endothelial cells | orientation/coherency analysis | “alignment analysis was performed on 10 representative non-overlapping images for each shear condition using ImageJ with the OrientationJ plugin” |
| 282 | 2026 | Mousavi et al. (2026) Heart-On-a-Chip with Integrated Ultrasoft Mechanosensors for Continuous Measurement of Cell- and Tissue-Scale Contractile Stresses Small · doi:10.1002/smll.202504493 | cardiac tissue engineering | Distribution (directionality histogram) + structure-tensor order parameter | “Cell alignment was evaluated using the OrientationJ plugin by generating orientation histograms and calculating the Orientational Order Parameter (OOP).” |
| 283 | 2026 | Cheah et al. (2026) Customizable Fabrication of 2D and Conformal Multielectrode Arrays for 3D Printed Organotypic Bioelectronic Interfaces Advanced Healthcare Materials · doi:10.1002/adhm.202502757 | cell alignment in bioelectronic tissue | orientation/coherency analysis | “Image analysis was performed on FIJI‐J using the OrientationJ plugin to determine cell alignment.” |
| 284 | 2026 | Bathe-Peters et al. (2026) Effects of altered gravity on adrenergic-mediated cAMP signalling in intact cells npj Microgravity · doi:10.1038/s41526-026-00587-z | cell membrane cytoskeleton architecture | orientation/coherency analysis | “Extraction of orientation analysis using OrientationJ for control and µg conditions at the basolateral membrane and a plane through the perinuclear region” |
| 285 | 2026 | Aitken et al. (2026) Ovarian Fibrosis Through Comparative Analysis of Collagen Architecture Molecular Reproduction and Development · doi:10.1002/mrd.70107 | collagen/ECM in ovarian fibrosis | Coherency map | “images were analyzed using the OrientationJ plugin to generate a coherency map and calculate the directional coherency coefficient” |
| 286 | 2026 | Corsini et al. (2026) Aberrant VEGFR2 supports tumor growth by extracellular matrix remodeling Cell Death & Disease · doi:10.1038/s41419-025-08404-3 | collagen/ECM in tumors | Distribution (directionality histogram) | “we investigated the fibril orientation in ECM in Sk-Mel-31 and OVCAR3-derived tumor sections using the OrientationJ plugin of ImageJ, which provide a visual representation of fibril orientation distribution” |
| 287 | 2026 | Karunaseelan et al. (2026) Multi-axial strain mapping to characterise structure and material properties of the human hip capsule PLOS One · doi:10.1371/journal.pone.0343718 | connective tissue biomechanics | structure tensor & coherency analysis | “The local orientation and isotropic properties of the fibrous structures were derived from a 2 x 2 symmetric structure tensor generated for each pixel using ImageJ software and the OrientationJ plugin” |
| 288 | 2026 | Zhou et al. (2026) Immunomodulatory cytoskeleton of bionic periosteum affects mitochondrial dynamics to promote osteogenesis Bioactive Materials · doi:10.1016/j.bioactmat.2026.05.041 | electrospun fibers, bone tissue engineering | Distribution (directionality histogram) | “We used the OrientationJ Distribution tool to quantify the percentage of different groups of electrospun fibres in each angular orientation.” |
| 289 | 2026 | Vihmar et al. (2026) Fibrous contextual embodiments formed by task-invariant continuous blow spinning in dynamic environments Frontiers in Robotics and AI · doi:10.3389/frobt.2026.1736915 | materials/nanofibers | Distribution (directionality histogram) | “Fiber orientation distributions were measured using the ImageJ plugin OrientationJ.” |
| 290 | 2026 | Marcelin et al. (2026) Localized Delivery of a Small Molecule Hedgehog Agonist via Poly(ε‐caprolactone) Scaffolds Enhances Tendon‐to‐Bone Integration DOI pending | materials/nanofibers | orientation/coherency analysis | “Fiber diameter and fiber alignment were calculated from 4 images (2574×) from these locations using the General Image Fiber Tool (GIFT) [ 26 ] and OrientationJ plugin in FIJI” |
| 291 | 2026 | Livrinska et al. (2026) Bacterial Nanocellulose Wound Dressings with Gentamicin-Loaded Chitosan Nanoparticles for Surgical Site Infection Management DOI pending | materials/nanofibers | orientation/coherency analysis | “The orientation of the fibers was determined using the OrientationJ plugin [ 31 ] to the ImageJ software 1.51w.” |
| 292 | 2026 | Dos et al. (2026) Insights into Structural Transformation during Oxidative Stabilization of Pan Nanofibers Reinforced with Carbon Nanotubes and Graphene Nanoplatelets ACS Polymers Au · doi:10.1021/acspolymersau.6c00010 | materials/nanofibers | Distribution (directionality histogram) | “The orientation distribution was quantified from SEM micrographs and obtained using OrientationJ” |
| 293 | 2026 | Oosthuysen et al. (2026) Electrospun poly-4-hydroxybuterate scaffolds enable local zero-order estradiol delivery and promote collagen maturation in a hypoestrogenic rat model for pelvic organ prolapse repair Biomaterials and Biosystems · doi:10.1016/j.bbiosy.2026.100133 | materials/nanofibers | Fiber orientation analysis | “Fiber diameter and orientation, and pore size (n=6) were determined from SEM images using open source image processing software Fiji with DiameterJ and OrientationJ plugins.” |
| 294 | 2026 | Trifan et al. (2026) MAPLE Deposition of Resorbable Calcium Phosphates on Electrospun Nylon Nanofibres for Bone Tissue Engineering Materials · doi:10.3390/ma19112375 | materials/nanofibers | Distribution (directionality histogram) | “Fibre orientation was quantified on low-magnification SEM micrographs using the OrientationJ plugin implemented in Fiji.” |
| 295 | 2026 | Liu et al. (2026) Topology-optimized melt-electrowritten PCL patch for abdominal wall reconstruction Bioactive Materials · doi:10.1016/j.bioactmat.2025.09.026 | materials/nanofibers | Distribution (directionality histogram) | “the feature "OrientationJ Distribution" was executed with an object size of one pixel and the cubic spline gradient with the parameters of 60 % coherence and 1 % energy.” |
| 296 | 2026 | Tort et al. (2026) AI-Driven Image Analysis for Nanofiber Characterization: From Diameter Measurement to Multiparameter Assessment ACS Omega · doi:10.1021/acsomega.5c12433 | materials/nanofibers | Distribution (directionality histogram) | “The orientation and diameter of the fibers were determined using OrientationJ and DiameterJ, respectively.” |
| 297 | 2026 | Kamel et al. (2026) Engineering a Compartmentalized Multi-Cell Co-Culture Hydrogel System Using Beeswax/Fucoidan/Alginate for Cultured Meat Modeling Foods · doi:10.3390/foods15101715 | muscle tissue engineering, cultured meat | Distribution (directionality histogram) | “The relative frequency (%) of myotube orientation was determined using the OrientationJ plugin (Version 2.0.7)” |
| 298 | 2026 | Spagnuolo et al. (2026) Bioprinting of Microtissues Within Mechanically Tunable Support Baths to Engineer Anisotropic Musculoskeletal Tissues Advanced Science · doi:10.1002/advs.202509313 | musculoskeletal tissue engineering | Coherency map | “Collagen fibril orientation, dispersion, and coherency were analyzed using the OrientationJ and Directionality plugins in ImageJ.” |
| 299 | 2026 | Morita et al. (2026) Nanofiber-based platform for quantitative analysis of human oligodendrocyte ensheathment with pharmacological perturbations Stem Cell Reports · doi:10.1016/j.stemcr.2026.102923 | neuronal alignment and nanofibers | Orientation/coherency analysis | “The orientation of CLDN11 and nanofibers was quantified using the ImageJ OrientationJ plugin (NIH, Bethesda, MD, USA).” |
| 300 | 2026 | Ferro et al. (2026) Fn14 is an activity-dependent, Bmal1-regulated cytokine receptor that induces rod-like microglia and restricts neuronal activity in vivo Cell Reports · doi:10.1016/j.celrep.2026.116926 | neuronal microglia alignment | Dominant Direction | “we applied the ImageJ plug-in OrientationJ to assess the orientation of these tubular microglia relative to the dendrites of PYR neurons” |
| 301 | 2026 | Masuda et al. (2026) Orientation-based evaluation of scleral collagen fibers in uveitic secondary glaucoma Graefe's Archive for Clinical and Experimental Ophthalmology · doi:10.1007/s00417-025-07112-0 | scleral collagen fibers in glaucoma | Coherency and energy metrics | “Local two-dimensional fiber orientations were quantified using OrientationJ, with coherency (an index of local structural anisotropy) and energy (an index reflecting the magnitude of orientation information) as outcome variables.” |
| 302 | 2026 | Gohel et al. (2026) A non-transcriptional mitotic function of POU/Oct factors ensures spindle assembly and chromosome segregation Journal of Cell Science · doi:10.1242/jcs.264165 | spindle microtubule organization | Coherency map | “Spindle MT organization was quantified from α-tubulin images using the OrientationJ coherency index in Fiji/ImageJ, which reports local filament alignment (0=random, 1=perfectly ordered)” |
| 303 | 2026 | Xue et al. (2026) Mechanically preconditioned stem cells therapy using bioinspired liver-mimetic microspheres for functional liver repair Bioactive Materials · doi:10.1016/j.bioactmat.2026.05.025 | stem cells and liver tissue engineering | Dominant Direction | “Filament orientation was analyzed with the OrientationJ plugin, using the cell axis as 0° reference.” |
| 304 | 2026 | Fahad et al. (2026) Ex vivo endothelialized cECM-enriched core-shell fibrous vascular graft promotes rapid regenerative remodeling in vivo Bioactive Materials · doi:10.1016/j.bioactmat.2026.03.040 | vascular graft fiber alignment | orientation/coherency analysis | “Anisotropy of the fiber alignment was evaluated using the OrientationJ plugin.” |
The publications that the plugin authors ask users to cite, as listed on the official page and in the GitHub README:
Selected threads on the Scientific Community Image Forum where OrientationJ usage, parameters and interpretation are discussed — several answered with input from the plugin author:
This reference table was compiled and curated with the assistance of artificial intelligence. The core table (304 publications, 2013–2026) results from an AI-assisted full-text search of the scientific literature for explicit mentions of the ImageJ/Fiji plugin “OrientationJ”: for each publication, the sentence describing how the plugin was used (“usage extract”) was taken from the article text, the OrientationJ mode and field of application were classified from that context, and the bibliographic metadata (title, journal, authors, DOI) were collected from the publishers’ records. The appendix of additional resources was compiled by Claude (Anthropic) on 7 August 2026 through targeted web searches of the image.sc forum (forum.image.sc), GitHub and GitLab repositories, the EPFL Biomedical Imaging Group website (bigwww.epfl.ch), PyPI/bioconda and publisher databases (PubMed, publisher pages); the DOIs of the four primary references were cross-checked against PubMed and the publishers. Automated quality checks were run on the table: all DOIs match the standard DOI pattern, no duplicate DOIs were found, and three 2026 entries (Zhao et al., Marcelin et al., Livrinska et al.) currently lack a DOI/journal (in press or preprint at the time of compilation; Zhao et al. appears in Bioactive Materials). AI-assisted compilation can contain errors — please verify quotes and DOIs against the original articles before formal citation.
Last updated: 7 August 2026.