list of software

	identifier	has function	has topic	Requires
Segmentation and Tracking of Mammary Epithelial Organoids in Brightfield Microscopy	1862	Cell segmentation, Cell tracking, Synthetic image generation	Live sample imaging, Bright field microscopy, Machine learning	ImageJ
OrganoSeg	1861	Cell segmentation, Object feature extraction	Bright field microscopy, DIC microscopy, Phase contrast microscopy	Matlab Image Processing Toolbox
OrganoID	1860	Cell segmentation, Object feature extraction, Object tracking	Live sample imaging, Bright field microscopy, Phase contrast microscopy, Machine learning	Python
JIPipe: visual batch processing for ImageJ	1859	Image processing	Bioimage informatics	Maven
Fractal	1849	Image analysis, Image segmentation, Data handling, Illumination correction, Visualisation	Bioimage informatics, High content screening, Machine learning
Nuclei Segmentation (Stardist)	1846	Cell segmentation	Machine learning
Nuclei Segmentation (Cellpose)	1845	Cell segmentation	Machine learning
MiNA - Mitochondrial Network Analysis	1844	Image analysis, Image thresholding, Morphological operation, Skeletonisation	Bioimage informatics, Fluorescence microscopy	ImageJ
MosaicExplorerJ	1843	Data handling, Image stitching	Light-sheet microscopy	ImageJ
Incucyte Base Analysis Software	1838	Analysis, Cell segmentation, Image visualisation	Live sample imaging, Fluorescence microscopy, Phase contrast microscopy, Machine learning
ImageJ Threshold	1837	Image thresholding		ImageJ
Semi-automated quantification of three stages of phagocytosi using ImageJ	1836	Cell segmentation, Interactive segmentation, Object classification	Fluorescence microscopy, Bright field microscopy	ImageJ
FluoGAN	1835	Image reconstruction, Image deconvolution	Widefield microscopy, Confocal fluorescence microscopy	Python, PyTorch
Relate	1825	Image registration, Image analysis, Image segmentation, Particle tracking, Image deconvolution, Image denoising, Visualisation, Overlay, Slice rendering, Surface rendering, Plotting	Correlative Light and Electron Microscopy, Electron microscopy, Scanning electron microscopy, Cryo scanning electron microscopy, Focused ion beam scanning electron microscopy, Serial block-face scanning electron microscopy, Transmission electron microscopy, Scanning transmission electron microscopy, Light microscopy, Point-scanning microscopy, Multimodal imaging, Spectroscopy, Statistics
Junction Mapper	1823	Analysis, Filament tracing, Object feature extraction, Shape features	Fluorescence microscopy, Confocal fluorescence microscopy
SynActJ	1816	Neuron image analysis	Live sample imaging	Fiji
Point Cloud Analyst (PoCA)	1788	Analysis, Colocalisation analysis, Object-based colocalisation, Cell segmentation, Interactive segmentation, Visualisation	Super-resolution microscopy, Single molecule localization microscopy
Orthanc	1782	Data handling, Image visualisation	Magnetic resonance imaging, Multimodal imaging, Positron emission tomography, Ultrasonography
Correlia	1712	Image registration, Affine registration, Deformable registration, Visualisation	Correlative Light and Electron Microscopy, Multimodal imaging	ImageJ
empanada-napari	1689	Image segmentation, Cell segmentation	Electron microscopy, Machine learning	Napari image viewer
MIA	1688	Image registration, Image analysis, Image segmentation, Object counting, Object detection, Object tracking, Morphological operation, Image visualisation		Fiji, MorphoLibJ
ASTEC	1686	Cell segmentation, Drift correction	Light-sheet microscopy
ClearMap	1685	Alignment construction, Image registration, Image analysis, Filament tracing, Cell segmentation, Neuron image analysis, Data handling, Image stitching, Visualisation	Light-sheet microscopy	OpenCV, scikit-image
BaSiC	1684	Image correction	Light microscopy, Fluorescence microscopy	Fiji
Voxelytics-Align	1683	Alignment construction, Image reconstruction, Image stitching	Electron microscopy, Serial block-face scanning electron microscopy	webKnossos: 3D image annotation, visualization and sharing
hot-knife	1682	Alignment construction, Data handling, Image stitching, Geometric distortion correction	Electron microscopy, Focused ion beam scanning electron microscopy
Render	1681	Alignment construction, Feature-based registration, Object feature extraction, Data handling, Image stitching, Visualisation, Image visualisation, Montage	Data sharing, Electron microscopy, Scanning electron microscopy	ImgLib2
EVER-ImageJ-Plugin	1680	Image processing	Single molecule localization microscopy	ImageJ
pyTFM	1679	Collective object tracking	Bioimage informatics	Python
napari-pyclesperanto-assistant	1678	Image analysis	Bioimage informatics
AnnotatorJ	1672	Image annotation	Machine learning	Fiji
NDPI Export Regions Tool	1671	Data handling	Digital histology	ImageJ
APEER	1670	Analysis, Image segmentation, Cell segmentation, Model-based segmentation, Pixel classification, Annotation, Data handling, Image denoising	Imaging, Microscopy, Machine learning
Phindr3D	1666	Analysis, Image analysis, Image classification, Image feature detection, Neuron image analysis, Classification, Clustering, Image processing, Pattern recognition, Visualisation	Bioimage informatics, High content screening, Machine learning, Statistics	MATLAB
DeepCLEM	1665	Image registration, Affine transformation	Correlative Light and Electron Microscopy, Multimodal imaging	Fiji, Register Virtual Stack Slices (Fiji), CSBDeep a toolbox for Content-aware Image Restoration (CARE) in Fiji
Analyze Spheroid Cell Invasion In 3D Matrix	1664	Cell segmentation, Object counting	Live sample imaging, Widefield microscopy, Fluorescence microscopy	MorphoLibJ
Analyze Complex Roots Tool	1663	Image analysis, Image segmentation		Fiji
Local Z Projector	1662	Image processing	Live sample imaging, Confocal fluorescence microscopy	ImgLib2, ImageJ 2.x
Effective image visualization for publications – a workflow using open access tools and concepts	1661
webKnossos: 3D image annotation, visualization and sharing	1660	Image segmentation, Interactive segmentation, Neuron image analysis, Image annotation, Data handling, Skeletonisation, Image visualisation, Overlay, Slice rendering, Volume rendering	Data sharing, Magnetic resonance imaging, Electron microscopy, Fluorescence microscopy, Tomography
Viv	1659	Visualisation, Image visualisation, Overlay, Slice rendering	Data sharing, Imaging, Microscopy
BTrackMate	1658
A simple MSER based segmentation tool for spot detection in 2/3/4D.	1657
LaRoME	1656	Image analysis	Bioimage informatics
QuantiFish	1655	Image registration, Image thresholding, Object counting, Object detection	Imaging, In-vivo imaging, Light microscopy, Fluorescence microscopy
HistoCAT	1653	Analysis, Cell segmentation, Clustering	Digital histology, Fluorescence microscopy
NDPItools	1652	Image generation	Digital histology	ImageJ
ndpi_extractroi	1651	Image generation	Digital histology	OpenSlide
Image-classification with deep learning in KNIME	1650	Image classification	Bioimage informatics
Qualitative annotations Fiji plugins	1649	Image classification, Object classification, Annotation, Image annotation	Bioimage informatics	ImageJ, Fiji
3D Nuclei Clustering Tool	1648	Clustering	Fluorescence microscopy	ImageJ
Interactive features visualization in KNIME	1647	Classification, Clustering, Visualisation	High content screening, Statistics
MoBIE-Utils-Python	1646	Data handling	Data sharing, Multimodal imaging
MoBIE Fiji Viewer	1645	Visualisation, Image visualisation	Data sharing, Correlative Light and Electron Microscopy, Electron microscopy, Light microscopy, Multimodal imaging	Fiji, BigDataViewer
nd-safir	1642	Image denoising	Widefield microscopy, Fluorescence microscopy, Confocal fluorescence microscopy
ROI 1-click tools for ImageJ/Fiji	1641	Annotation, Image annotation	Bioimage informatics	ImageJ, Fiji
SPHIRE	1640
CAREless	1639	Image deconvolution, Image denoising, Image enhancement	Microscopy, Machine learning	ImageJ, Python
ImageM	1637	Image analysis, Image segmentation, Data handling, Image visualisation	Bioimage informatics	Matlab Image Processing Toolbox, MATLAB, MATLAB Statistics toolbox
InSegt	1636	Interactive segmentation, Pixel classification, Texture extraction, Clustering	Bioimage informatics, Machine learning	MATLAB
BioImage Model Zoo	1635	Image classification, Cell segmentation, Image denoising	Digital histology, Electron microscopy, Light microscopy, Fluorescence microscopy, Machine learning
Yapic	1634	Pixel classification	Machine learning, Supervised learning
LobSTer	1633
Piximi	1632	Image classification	Machine learning
StarDist - ImageJ	1631	Image segmentation, Cell segmentation, Model-based segmentation	Light microscopy, Light-sheet microscopy, Fluorescence microscopy, Multi-photon microscopy, Machine learning	ImageJ
cellpose	1630	Cell segmentation	Machine learning	Python
DeepImageJ	1629	Cell segmentation, Image denoising	Machine learning	ImageJ, Tensorflow
IR tools	1628	Optimisation or refinement	Bioimage informatics	MATLAB
MorphoNet Python API	1627	Annotation, Validation, Visualisation	Bioimage informatics, Data sharing	MorphoNet
MorphoNet	1626	Annotation, Image annotation, Landmark assignment, Visualisation, Image visualisation, Surface rendering	Bioimage informatics, Data sharing
VAST Lite	1625	Image segmentation, Cell segmentation, Object classification, Annotation, Image annotation	Microscopy, Electron microscopy, Focused ion beam scanning electron microscopy, Serial block-face scanning electron microscopy
Neuron Tracing Vaa3D (BJUT FM Spanning Tree)	1623	Filament tracing, Neuron image analysis		Vaa3D
Filament Tracing LocThresh (ImageJ)	1622	Filament tracing, Local thresholding, Skeletonisation		ImageJ
Filament Tracing Tubeness (ImageJ)	1621	Filament tracing, Feature enhancement, Skeletonisation		ImageJ, Tubeness
Neuron Tracing Vaa3D (MOST)	1620	Filament tracing, Neuron image analysis		Vaa3D, MOST-Raytracer
Neuron Tracing Vaa3D (MST)	1619			Vaa3D
Neuron Tracing 3D (Rivuletpy)	1618	Filament tracing, Neuron image analysis
Neuron Tracing Vaa3D (App2)	1617	Filament tracing, Neuron image analysis		Vaa3D, APP2
Object Tracking (MU-Lux-CZ)	1616	Object tracking	Machine learning	OpenCV, scikit-image, Tensorflow, Keras
Object Tracking (Octave)	1615	Object tracking		GNU Octave
Object Tracking (ImageJ)	1614	Object tracking		ImageJ
pyimagej	1612	Image processing	Bioimage informatics	Python
Nuclei Tracking (TrackMate)	1613	Particle tracking		TrackMate, pyimagej
Particle Tracking (ImageJ)	1611	Particle tracking		ImageJ, FeatureJ Laplacian
Nuclei Segmentation 3D (NucleiSegmentation3D-ilastik)	1610	Pixel classification	Machine learning	ilastik
Nuclei Segmentation 2D watershed (NucSeg3DThr-ImageJ)	1609
Nuclei Segmentation (U-Net)	1608		Machine learning	scikit-image, NumPy
Nuclei Segmentation (DeepCell)	1607		Machine learning	scikit-image, SciPy, NumPy, matplotlib, Libtiff, scikit-learn (sklearn)
FeatureJ Hessian	1605
Spot Detection 3D Hessian (ImageJ)	1606			ImageJ, FeatureJ Laplacian, ImageJ Built-in Macro Functions, FeatureJ Hessian
Spot Detection 3D (Icy)	1604	Spot detection		Icy
Spot Detection Dmap (ImageJ)	1603	Spot detection, Distance transform		ImageJ, FeatureJ Laplacian, ImageJ Built-in Macro Functions
3D cell tracking using Gaussian Mixture Model (TGMM)	1600	Cell tracking	Bioimage informatics, Live sample imaging, Light-sheet microscopy
PSFj	1599	Optimisation or refinement	Microscopy
NucleusJ	1598	Image segmentation	Bioimage informatics	Fiji, MorphoLibJ
Amira / Avizo Xtra library	1597			Amira
Epina Image Lab	1596	Alignment construction, Image registration, Image analysis, Image processing	Multimodal imaging
QuickFit 3	1595	Image analysis, Plotting	Fluorescence correlative spectroscopy, Image correlation spectroscopy
Replace Red with Magenta	357	Image correction		ImageJ
Napari image viewer	1594	Visualisation, Image visualisation, Volume rendering	Bioimage informatics, Imaging
OligoMacro Toolset	1593	Image analysis, Cell segmentation, Cell tracking, Plotting	Live sample imaging, In-vitro imaging, Widefield microscopy, Transmission light microscopy, Phase contrast microscopy	StackReg, TurboReg
MATLAB Wavelet toolbox	1592	Frequency analysis, Image feature detection, Synthetic image generation, Image processing	Bioimage informatics	MATLAB
automated structures analysis program (ASAP)	1591
Icy Spot Tracking	1590	Particle tracking, Trajectory analysis	Bioimage informatics, Machine learning	Spot Detector (Icy), Spot detection utilities, Track Manager
Icy Label Extractor	1589	Object classification	Bioimage informatics
Image registration in Matlab with Image Processing Toolbox	1588	Alignment construction, Image registration, Affine registration, Rigid registration, Deformable registration, Feature-based registration, Frequency analysis	Multimodal imaging	Matlab Image Processing Toolbox, Matlab Computer Vision System Toolbox
Adaptive Pixel Representation	1587	Conversion	Bioimage informatics
Mathematica	1586	Image processing, Visualisation	Machine learning, Statistics
LBADSA	1585	Image segmentation	Bioimage informatics	ImageJ
DropSnake	1584	Active contours	Bioimage informatics	ImageJ
FastSME	1583	Image projection	Microscopy
SME	1582	Image projection	Microscopy
DeepCell	1578	Cell segmentation, Cell tracking, Morphological operation	Fluorescence microscopy, Phase contrast microscopy	Tensorflow, Keras
DragonFly	1572	Image feature detection, Image segmentation, Interactive segmentation, Object feature extraction, Shape features, Visualisation, Image visualisation, Volume rendering	Digital histology, Electron microscopy, Light microscopy, Multimodal imaging, Machine learning
Neuroglancer	1570	Data handling, Visualisation, Image visualisation	Data sharing, Electron microscopy, Light-sheet microscopy
3D Segmentation & visualization of nanoparticles attached to the surface of red blood cells	1568	Object feature extraction	Fluorescence microscopy	ImageJ
Using ImageJ to Analyze the Size, Shape, and Directionality of Networks of Coupled Astrocytes	1566	Object feature extraction	Bioimage informatics, Confocal microscopy	Fiji
WormScan	1562			Fiji
Ikosa	1561	Image annotation, Data handling	Data sharing, Machine learning
Protein Array Analyzer for ImageJ	1560	Image analysis, Illumination correction	Bioimage informatics	ImageJ
Multi-Template matching	1557	Object detection, Pattern recognition	Bioimage informatics, High content screening	Fiji
FPBioimage	1556	Visualisation	Bioimage informatics
PYME	1555	Single molecule localisation, Visualisation	Bioimage informatics	Python 2.7
Filopodyan	1553	Image analysis, Filament tracing, Object tracking	Fluorescence microscopy	ImageJ, Fiji
CellProfiler Analyst CPA	1527	Image analysis, Image classification, Visualisation	High content screening, Statistics
Image Data Explorer	1496	Annotation, Visualisation	Bioimage informatics
EvaluateSegmentation Tool	1493			ITK, CMake
Snakemake	1491
Automated workflow for parallel Multiview Reconstruction	1492	Image registration, Image deconvolution, Selective plane illumination microscopy reconstruction, Image processing, Drift correction	Light-sheet microscopy	Fiji, Snakemake
YeastSpotter	1490	Cell segmentation	Bioimage informatics	Python
MSRC Registration Toolbox	1489	Image registration, Feature-based registration	Fluorescence microscopy, Multimodal imaging
Nuclei Segmentation (ilastik)	1488	Pixel classification	Machine learning	ilastik, scikit-image, SciPy, NumPy
Mask-RCNN	1486	Image segmentation, Object detection	Phase contrast microscopy	Tensorflow, Keras, Python 3.6
Nuclei Segmentation (Mask-RCNN)	1487	Image segmentation, Object detection	Machine learning
Landmark detection DMBL model prediction	1485	Landmark assignment	Machine learning	scikit-learn (sklearn), Python 3.6, sumproduct
sumproduct	1483		Machine learning	Python
Landmark detection DMBL model training	1484	Landmark assignment	Computerized tomography	scikit-learn (sklearn), Python 3.6, sumproduct
Landmark detection LC models prediction	1482	Landmark assignment	Machine learning	scikit-learn (sklearn), Python 3.6
Landmark detection LC models training	1481	Landmark assignment	Machine learning	scikit-learn (sklearn), Python 3.6
Landmark detection MSET models prediction	1480	Landmark assignment	Machine learning	Python, scikit-learn (sklearn)
Landmark detection MSET models training	1479	Landmark assignment		scikit-learn (sklearn), Python 3.6
pydensecrf	1478
PyTorch	1476		Machine learning	Python
Pixel classification for GlaS challenge with UNet	1477	Pixel classification, Smoothing		PyTorch, pydensecrf
ContourLines	1475		Bioimage informatics	ImageJ, Fiji
pyBPDL	1474	Image registration, Image analysis, Shape features		Python
BIRL	1473	Image registration	Multimodal imaging
jSLIC	1471	Image segmentation	Imaging	ImageJ
pyImSegm	1470	Image segmentation	Machine learning	Python
CMake	1468
VascuSynth	1469	Image generation		ITK, CMake
Nuclei Segmentation (CellProfiler)	1467	Image segmentation		CellProfiler
Nuclei Tracking (ImageJ)	1466	Object tracking		ImageJ
3D Fill holes (mcib3d)	1464	Morphological operation		mcib3d library, ImageJ
Maximum (3D) VIB Protocol	1463	Image convolution, Morphological operation		ImageJ, VIB Protocol
Neuron Tracing 3D (ImageJ)	1465	Filament tracing, Neuron image analysis, Feature enhancement		ImageJ
Nuclei Segmentation (Python)	1462	Adaptative thresholding, Watershed segmentation, Object detection, Smoothing		scikit-image, SciPy, NumPy
ROI Measure for Icy	1460	Image analysis	Bioimage informatics	Icy
Spot Detection (Icy)	1461	Spot detection
Minimum (3D) Filter VIB Protocol	1457	Image convolution		VIB Protocol
Spot Detection 3D (ImageJ)	1458	Spot detection		ImageJ, FeatureJ Laplacian, Analyze Particles
ImageJ Built-in Macro Functions	1455		Bioimage informatics	ImageJ
Spot detection (ImageJ)	1456	Spot detection		ImageJ, FeatureJ Laplacian, Find Maxima, ImageJ Built-in Macro Functions
Thresholder (ImageJ)	1454	Image segmentation, Image thresholding		ImageJ
Filament Tracing (ImageJ)	1453	Filament tracing, Smoothing, Skeletonisation		ImageJ
FandPLimitTool	1452	Image generation, Synthetic image generation	Single molecule localization microscopy
NVidia CUDA 9	1449
Holovibes	1450	Generation, Image generation, Image reconstruction	Microscopy, Light microscopy, Widefield microscopy, Phase contrast microscopy	NVidia CUDA 9
autoQC	1447
mamut2r	1445	Analysis
ImJoy	1444	Object classification, Classification, Prediction and recognition	Machine learning
NanoJ	1443	Image registration, Image analysis, Image processing, Image correction	Live sample imaging, Fluorescence microscopy, Super-resolution microscopy	ImageJ
HAWK	1442	Image processing, Image correction	Fluorescence microscopy, Super-resolution microscopy	ImageJ
Nuclei Segmentation 3D Watershed (NucleiSegmentation3D-ImageJ)	1441	Image segmentation, Watershed segmentation, Smoothing		ImageJ
3D ImageJ Suite	1440	Colocalisation analysis, Image segmentation, Object feature extraction, Morphological operation, Visualisation	Bioimage informatics	ImageJ, ImageScience.jar
Gaussian Blur 3D (ImageJ)	1439	Image convolution, Smoothing		ImageJ
Watershed (ImageJ ij-1.52i)	1437	Watershed segmentation
Nuclei Segmentation 2D (ImageJ)	1438	Image segmentation, Watershed segmentation		ImageJ
Resolving the process of Clathrin mediated endocytosis using Correlative Light & Electron Microscopy (CLEM)	1436
Motility analysis with mean-square displacement	1435
The NEMO dots assembly: Single-particle tracking and analysis	1433
3D vessel segmentation of synchrotron phase contrast tomography	1432	Image analysis	Bioimage informatics, Tomography, Machine learning
CRImage	1431	Classification	Digital histology, High content screening, Bright field microscopy	R
clij2	1430	Spot detection, Image thresholding, Local thresholding, Object counting, Image deconvolution, Image denoising, Image projection, Affine transformation, Linear transformation, Rotation, Image crop, Smoothing, Closing, Dilation, Erosion, Opening, Volume rendering	Bioimage informatics, Statistics	Fiji, Icy, MATLAB
Chromagnon	1429	Chromatic aberration correction	Fluorescence microscopy
Daybook2	1428		Fluorescence microscopy
ConfocalCheck	1427		Fluorescence microscopy	ImageJ
MIPs for PSFs	1425	Image analysis, Image visualisation	Bioimage informatics	ImageJ, Fiji
MetroloJ	1424		Fluorescence microscopy	ImageJ
MeVisLab XMarkerShortestPath module (Dijsktra shortest path)	1423	Analysis, Shape features		MeVisLab
BoneJ	1422	Skeletonisation		ImageJ
MeVisLab	1421	Image registration, Image segmentation, Morphological operation, Visualisation, Volume rendering	Magnetic resonance imaging, Tomography, Computerized tomography
Spimagine	1419	Visualisation	Light-sheet microscopy	OpenCL
TEM ExosomeAnalyzer	1418	Image segmentation, Image visualisation	Electron microscopy
Registrationshop	1417	Image registration, Affine registration, Rigid registration, Deformable registration, Visualisation	Multimodal imaging	elastix
SODA suite	1416	Colocalisation analysis, Pixel-based colocalisation	Bioimage informatics, Confocal fluorescence microscopy, Super-resolution microscopy	Icy
PartSeg	1415	Image segmentation, Cell segmentation, Interactive segmentation, Object feature extraction	Bioimage informatics
AssayScope	1414	Analysis, Image segmentation, Cell segmentation	Digital histology, Statistics
Python 3.6	1413
​The Allen Cell Structure Segmenter	1412	Image segmentation, Interactive segmentation	Bioimage informatics	Python 3.6
DeconvolutionLab2	1411	Image deconvolution	Microscopy	ImageJ
GaussFit OnSpot	1409	Spot detection		ImageJ
Spots colocalization (ComDet)	1408	Colocalisation analysis, Spot detection	Bioimage informatics	ImageJ, Jama
PTA2	1406	Particle tracking	Bioimage informatics	Fiji
MiToBo	1404	Analysis, Image feature detection, Cell segmentation, Object detection, Object feature extraction, Visualisation	Bioimage informatics, Statistics	Fiji
HDomeTransform3D	1405	Spot detection, Morphological operation	Bioimage informatics	Fiji, MiToBo
Nessys	1403	Cell segmentation, Editing	Fluorescence microscopy, Confocal microscopy
FluoRender	1402	Image visualisation, Volume rendering	Confocal microscopy
3Dscript	1400	Image visualisation, Volume rendering		ImageJ
Labkit	1399	Image segmentation, Image annotation, Image visualisation	Machine learning	ImageJ
SciView	1398	Image visualisation		ImageJ
SQUIRREL	1397	Image analysis	Super-resolution microscopy, Single molecule localization microscopy, Statistics	ImageJ, NanoJ
InspectJ	1395	Image analysis, Pattern recognition, Image validation		ImageJ
JavaFX	1393
Maven	1394		Bioimage informatics
Paintera	1392	Filament tracing, Neuron image analysis, Image reconstruction, Image visualisation, Slice rendering, Surface rendering, Volume rendering	Electron microscopy, In-silico reconstruction	JavaFX, Maven
shinyHTM	1391	Visualisation, Image visualisation, Plotting	High content screening, Statistics
TTK the Topology Toolkit	1390	Analysis, Clustering, Visualisation	Statistics	Paraview
Paraview	1389	Visualisation, Image visualisation, Volume rendering
Icy-OpenCV	1388	Image processing	Bioimage informatics	EzPlug SDK
IJ-OpenCV	1387
Blender	1386	Image visualisation, Surface rendering, Volume rendering	Bioimage informatics
NeuroMorph	1385	Analysis, Object classification, Image annotation, Image visualisation, Volume rendering	Electron microscopy, Tomography	Blender
FishInspector	1382	Image feature detection, Edge detection, Object classification, Object detection, Object feature extraction, Image annotation, Pattern recognition	Bioimage informatics, High content screening, In-vivo imaging, Microscopy, Light microscopy, Widefield microscopy, Bright field microscopy
SpotDetectionIJ	1381	Spot detection	Microscopy	ImageJ, FeatureJ Laplacian, Find Maxima
Creating an ImageJ plugin / command	1380	Image processing	Bioimage informatics	ImageJ, Fiji, IntelliJ IDEA, Fiji
Jython for ImageJ	1379
IntelliJ IDEA	1377		Bioimage informatics
Eclipse	1378
scikit-learn (sklearn)	1376	Analysis, Prediction and recognition, Pattern recognition	Machine learning	Python, NumPy, matplotlib
3-D Density Kernel Estimation	1375	Pixel classification, Prediction and recognition, Object counting	Confocal microscopy, Machine learning	Jupyter notebook, Python, VIGRA, scikit-learn (sklearn), scikit-image
Microscope autopilot	1374	Image analysis	Light-sheet microscopy
Minimum cost Z surface projection	1371	Image projection	Microscopy, Fluorescence microscopy	Fiji
Interactive watershed	1370	Cell segmentation, Interactive segmentation, Watershed segmentation, Spot detection	Fluorescence microscopy	Fiji
Jupyter	1368
Jupyter notebook	1369		Bioimage informatics
ImageJ/FIJI	1364
Find Maxima (Python)	1367	Image analysis, Image feature detection		SciPy, PIL, Python, Jupyter, Jupyter notebook
2D Gaussian fitting macro (Fiji/ImageJ) for multiple signals.	1363	Image analysis, Single molecule localisation	Bioimage informatics, Single molecule localization microscopy	ImageJ, Fiji
Simple-Tracker	1360	Cell tracking, Particle tracking	Live sample imaging	MATLAB
FoCuS-point	1359	Analysis, Frequency analysis	Fluorescence microscopy, Fluctuation based microscopy, Fluorescence correlative spectroscopy, Point-scanning microscopy, Statistics
@msdanalyzer	1358	Trajectory analysis	Live sample imaging, Statistics	MATLAB Curve Fitting Toolbox, MATLAB
FoCuS-scan	1357	Frequency analysis, Analysis	Microscopy, Fluorescence microscopy, Spectroscopy
BioCat	1356	Image classification, Image annotation, Pattern recognition	Machine learning
FNIRT	1355	Image registration, Deformable registration	Magnetic resonance imaging	FMRIB's Linear Image Registration Tool FLIRT
FMRIB's Linear Image Registration Tool FLIRT	1354	Image registration, Linear transformation	Magnetic resonance imaging
acquiarium	1353	Spot detection, Chromatic aberration correction, Geometric distortion correction, Illumination correction	High content screening, Fluorescence microscopy, Confocal fluorescence microscopy
StainGAN	1352	Image correction	Digital histology, Widefield microscopy
3D-DAOSTORM	1351	Single molecule localisation	Super-resolution microscopy, Single molecule localization microscopy
ThreeB 3B Microscopy Analysis Software	1350	Single molecule localisation, Image deconvolution	Super-resolution microscopy	ImageJ
simpleITK	1347	Image registration, Image analysis, Image segmentation, Data handling, Image visualisation	Bioimage informatics
cython	1348		Bioimage informatics	Python
Rivulet 2 (Rivuletpy)	1349	Filament tracing, Image thresholding, Neuron image analysis, Distance transform		SciPy, NumPy, Python, Libtiff, simpleITK, cython
ZEN Blue	1345
ZEN and APEER Machine Learning Platform	1346	Image segmentation, Cell segmentation, Model-based segmentation, Pixel classification, Object classification	Digital histology, High content screening, Electron microscopy, Light microscopy, Fluorescence microscopy, Machine learning, Supervised learning	ZEN Blue, APEER
idr-py	1344
rOMERO-gateway	1343	Data handling	Bioimage informatics	OMERO.server
BisQue	1342	Image analysis, Data handling	Data sharing
Openimadis	1341	Data handling, Image annotation	Bioimage informatics, Data sharing	LOCI Bioformats plugin
ScientiFig	1340	Montage	Data sharing	Fiji
Fit a model for the growth of yeast cells	1339	Object counting, Analysis	High content screening, Fluorescence microscopy	EBImage, rOMERO-gateway
Cell or particle counting and scoring the percentage of stained objects	1338	Cell segmentation, Object classification, Object counting	Fluorescence microscopy	CellProfiler
Cell or particle Counting and scoring stained objects using CellProfiler	1337	Object classification, Analysis	Bioimage informatics, Fluorescence microscopy	Cell or particle counting and scoring the percentage of stained objects, idr-py
Quantification of outer ring diameters of centriole or PCM proteins of cycling HeLa cells in interphase	1336	Object detection, Object feature extraction, Analysis	High content screening, Fluorescence microscopy, Structured illumination microscopy	ImageJ, R Project for Statistical Computing, Maximum Entropy Threshold (ImageJ), Analyze Particles, OMERO.insight-ij client
pystackreg	1333	Alignment construction, Image registration, Affine registration, Rigid registration	Electron microscopy, Fluorescence microscopy	StackReg, TurboReg
Detection of Molecules - DoM	1332	Single molecule localisation, Chromatic aberration correction, Drift correction	Super-resolution microscopy	ImageJ
Aivia - Aivia Cloud - Aivia Web	1331	Analysis, Frequency analysis, Image analysis, Colocalisation analysis, Object-based colocalisation, Pixel-based colocalisation, Filament tracing, Image feature detection, Image segmentation, Cell segmentation, Pixel classification, Neuron image analysis, Object classification, Object counting, Texture extraction, Object tracking, Cell tracking, Particle tracking, Annotation, Classification, Editing, Image deconvolution, Visualisation, Image visualisation, Volume rendering, Plotting	Machine learning
JDK	1329
Fourier Bandpass Filter	1326			ImageJ
Temporal Medial Filter	1327
Python 2.7	1323	Analysis, Data handling, Image processing, Visualisation, Plotting	Bioimage informatics, Machine learning, Statistics
Chainer	1324		Machine learning	Python
QCAnet	1325	Image segmentation	Fluorescence microscopy, Machine learning	Python 2.7, Chainer, matplotlib, NumPy, scikit-image
bftools	1319
GNU Parallel	1320
ImageMagick	1321
Libtiff	1322	Data handling	Bioimage informatics
MATLAB Signal Processing Toolbox	1318
matplotlib	1317	Data handling, Visualisation, Plotting	Bioimage informatics	Python
Manual tracking with TrackMate	1316	Object tracking		Fiji
GIMP	1315	Conversion, Image processing
Log3D	1314	Spot detection, Image processing, Image convolution		ImageJ
ImagePy	1313	Image segmentation, Data handling, Image processing, Visualisation, Analysis	Bioimage informatics	Python
Python	1312	Analysis, Data handling, Image processing, Visualisation, Plotting	Bioimage informatics, Machine learning, Statistics
ImageScience.jar	1309
Jama	1310			JDK
Tracking2.0	1311	Object tracking, Particle tracking	Bioimage informatics	ImageJ, Jama
jMathPlot	1308
Quality metric of 3D SPIM stacks	1307		Light-sheet microscopy
BM3D denoising	1306
Spheroid simulator	1305
3D confocal noise simulator	1304
Mean shift	1303
PHANTAST for FIJI	1302	Cell segmentation	Phase contrast microscopy	Fiji
DEFCoN-ImageJ	1301	Spot detection, Object counting	Machine learning	Fiji
MATLAB Curve Fitting Toolbox	1300
LOCI Bioformats plugin	1299
Align slices in stack	1298	Image registration		ImageJ
Bioconductor	1297	Analysis	Bioimage informatics, High content screening
cvMatch_Template	1296	Image segmentation, Pattern recognition	Electron microscopy	ImageJ, OpenCV
Template Matching and Slice Alignment--- ImageJ Plugins	1294	Image registration		ImageJ, OpenCV
Excel	1293
CSBDeep a toolbox for Content-aware Image Restoration (CARE) in Knime	1292	Image deconvolution, Image denoising	Light microscopy, Light-sheet microscopy	KNIME
CSBDeep a toolbox for Content-aware Image Restoration (CARE) in Fiji	1291	Image reconstruction, Image deconvolution, Image denoising, Image projection, Selective plane illumination microscopy reconstruction	Light microscopy, Light-sheet microscopy	Fiji
MATLAB Optimization toolbox	1289
MATLAB Statistics toolbox	1290
SciPy	1286	Data handling, Image processing, Parameter optimisation	Bioimage informatics, Statistics	Python
PIL	1287
NumPy	1288	Data handling	Bioimage informatics	Python
R Project for Statistical Computing	1284
Neuroconductor	1285	Image segmentation	Bioimage informatics	R Project for Statistical Computing
CompuCell3D	1280	Synthetic image generation, Plotting	In-silico reconstruction
elastix	1278	Image registration, Affine registration, Deformable registration	Magnetic resonance imaging, Multimodal imaging, Computerized tomography
Cancer Imaging Phenomics Toolkit (CaPTk)	1277	Image registration, Image analysis, Image segmentation, Object feature extraction, Image enhancement, Image visualisation	Bioimage informatics
NiftyNet	1276	Image segmentation, Image generation, Synthetic image generation	Imaging, Magnetic resonance imaging, Machine learning	Tensorflow
Docker ParaViewWeb	1271	Visualisation, Image visualisation	Bioimage informatics	Galaxy Workbench for Image Analysis, Galaxy Image Analysis Tools
Galaxy Image Analysis Tools	1272	Image analysis	Bioimage informatics	Galaxy Workbench for Image Analysis, Docker ParaViewWeb
Galaxy Workbench for Image Analysis	1270		Bioimage informatics
Orbit	1225	Cell segmentation, Interactive segmentation, Object classification	Digital histology, Machine learning
HyphaTracker	1224	Image analysis, Filament tracing, Image segmentation, Object tracking, Drift correction, Image processing	Light microscopy, Bright field microscopy	ImageJ
LimeSeg	1223	Image segmentation		ImageJ
MAARS	1222	Cell segmentation, Object classification	Bright field microscopy, Machine learning	Micro-Manager
CEM	1221	Neuron image analysis, Dilation, Pixel-based colocalisation, Image feature detection, Colocalisation analysis	High content screening	ImageJ
MaMuT	1220	Image feature detection, Object tracking, Cell tracking, Image visualisation, Overlay, Plotting, Image annotation	Live sample imaging, Light-sheet microscopy	Fiji, BigDataViewer, TrackMate
Gaussian blur in ImageJ	1215	Image processing	Bioimage informatics	ImageJ
radial reslice	1216
kymograph generation	1217	Image analysis, Object tracking	Bioimage informatics	ImageJ
bleb dynamics	1218	Shape features, Cell tracking	Fluorescence microscopy, Confocal fluorescence microscopy	Gaussian blur in ImageJ, Otsu Thresholding, radial reslice, kymograph generation
Drishti	1214	Data handling, Visualisation, Image visualisation, Volume rendering	Electron microscopy, Electron tomography, Tomography
FlyLimbTracker	1213	Active contours, Interactive segmentation, Object tracking, Isolated object tracking	Microscopy, Fluorescence microscopy
THOT	1211	Trajectory analysis	Fluorescence microscopy, Confocal fluorescence microscopy, Single molecule localization microscopy, Statistics	MATLAB
Open Virtual stack in Fiji	1206
Create new TrakEM project in Fiji	1207
import images into TrakEM	1208
Spark Stitcher	1210	Image registration, Illumination correction, Image stitching	Light microscopy, Light-sheet microscopy	Fiji
Alignment of FIBSEM or SBFSEM images	1209			Fiji, Open Virtual stack in Fiji, TrakEM2, Create new TrakEM project in Fiji, import images into TrakEM, Linear Stack Alignment with SIFT (ImageJ)
Fiji CMTK GUI	1205	Image registration, Affine registration, Deformable registration	Imaging, Multimodal imaging	Fiji, CMTK
Z-spacing correction for Fiji	1204	Warping, Image correction	Electron microscopy	Fiji
Tensorflow	1201	Image classification, Image feature detection, Image segmentation, Image enhancement	Machine learning	Python
Keras	1202
Isotropic Super-Resolution for EM	1203	Image enhancement	Electron microscopy, Focused ion beam scanning electron microscopy, Machine learning	Tensorflow, Keras
MIPAV	1200	Image registration, Image analysis, Object-based colocalisation, Image segmentation, Image thresholding, Pixel classification, Smoothing, Image visualisation, Image feature detection, Colocalisation analysis	Bioimage informatics, Imaging, Magnetic resonance imaging, Computerized tomography
McLuigi	1199	Image segmentation, Object classification, Classification	Electron microscopy	VIGRA, Luigi
Luigi	1198	Data handling
ANTs: Advanced Normalization Tools	1197	Image registration, Affine registration, Rigid registration, Deformable registration, Image segmentation, Pixel classification, Illumination correction	Bioimage informatics	ITK
CMTK	1196	Image registration, Affine registration, Deformable registration, Image analysis, Image classification, Image processing	Bioimage informatics, Magnetic resonance imaging, Multimodal imaging, Statistics
Real-time multi-view deconvolution	1195	Image deconvolution, Selective plane illumination microscopy reconstruction
NBLAST	1194	Analysis, Clustering	Statistics	NeuroAnatomy Toolbox
TeraStitcher	1193	Alignment construction, Image registration, Rigid registration, Image stitching
NeuroAnatomy Toolbox	1192	Visualisation, Analysis	Bioimage informatics, Microscopy, Statistics
VMTK: Vascular Modeling Toolkit	1190	Image segmentation, Neuron image analysis, Visualisation, Volume rendering	Magnetic resonance imaging, Light-sheet microscopy	ITK
OpenCL	1186
ClearGL	1185	Visualisation	Bioimage informatics
ClearVolume	1183	Volume rendering	Microscopy, Light microscopy, Light-sheet microscopy	ClearCL, ClearGL
NeuroGPS-Tree	1187			Vaa3D
Shiny - R package	1177	Plotting	Data sharing, Statistics
ClearCL	1180	Image processing	Bioimage informatics	OpenCL
MicrotubuleTracker in FIJI	1175	Filament tracing, Object tracking, Trajectory analysis	In-vitro imaging	Fiji
Trakem2 lens distortion correction	1178	Geometrical transformation, Warping, Geometric distortion correction	Confocal microscopy	Fiji, TrakEM2
2D brain slice region annotation: SliceMap	1184	Image registration, Image segmentation	Widefield microscopy, Fluorescence microscopy
Globals for Images SimFCS 4	1173	Image analysis	Imaging, Microscopy, Fluorescence microscopy, Spectroscopy
scenery	1174	Visualisation	Bioimage informatics	ClearGL
Multiview Reconstruction	1176	Image registration, Affine registration, Rigid registration, Affine transformation, Chromatic aberration correction, Drift correction, Image deconvolution, Selective plane illumination microscopy reconstruction, Visualisation	Light-sheet microscopy	BigDataViewer, ImageJ, ImgLib2
BigDataViewer	1171	Image registration, Affine registration, Rigid registration, Visualisation, Image visualisation	Imaging, Light-sheet microscopy	ImgLib2
NeuriteTracer	1179	Filament tracing, Neuron image analysis, Image processing, Smoothing, Morphological operation, Skeletonisation	Fluorescence microscopy	ImageJ
intelligent Matrix Screener Remote Control	1170
SuRVoS	1172	Image segmentation, Interactive segmentation, Pixel classification, Prediction and recognition, Image annotation	Electron microscopy, Scanning electron microscopy, Focused ion beam scanning electron microscopy, Serial block-face scanning electron microscopy, Electron tomography, Cryo electron tomography, Machine learning
Bigwarp	1169	Image registration, Deformable registration, Warping	Correlative Light and Electron Microscopy, Electron microscopy, Multimodal imaging
BigStitcher	1168	Image registration, Affine registration, Rigid registration, Data handling, Affine transformation, Image deconvolution, Image stitching, Selective plane illumination microscopy reconstruction, Visualisation		ImageJ, ImgLib2, BigDataViewer
FracLac	1167		Bioimage informatics	ImageJ
MOST-Raytracer	1166	Filament tracing, Image segmentation, Image enhancement	Imaging, Tomography	Vaa3D
Simple Tracing DF-Tracing	1165	Filament tracing, Image segmentation, Adaptative thresholding, Neuron image analysis, Image enhancement, Distance transform		Vaa3D
OpenCV / Machine Learning	1164	Image analysis, Image segmentation, Classification	Machine learning	OpenCV
OpenCV / Image Stiching	1163	Image stitching	Bioimage informatics	OpenCV
OpenCV / Image Processing	1162	Image feature detection, Image thresholding, Watershed segmentation, Image processing, Geometrical transformation, Linear transformation, Smoothing, Morphological operation	Bioimage informatics	OpenCV
OpenCV / High-level GUI	1161	Data handling	Bioimage informatics	OpenCV
OpenCV / flann. Clustering and Search in Multi-Dimensional Spaces	1160	Classification, Clustering	Machine learning	OpenCV
OpenCV / Computational Photography	1159	Image processing	Bioimage informatics	OpenCV
OpenCV / Camera Calibration and 3D reconstration	1158	Image reconstruction	Bioimage informatics	OpenCV
OpenCV / CUDA	1157	Data handling		OpenCV
OpenCV / Biologically Inspired Vision Models and Derivative Tools	1156	Image enhancement, Feature enhancement	Bioimage informatics	OpenCV
OpenCV feature2d module	1155	Feature-based registration, Image analysis, Image feature detection, Object feature extraction, Object tracking	Bioimage informatics	OpenCV
R	1152
TIMP	1153			R
Wound Healing Tool	1150			ImageJ
Skin Tools	1149		Digital histology	ImageJ
nctuTW	1148	Neuron image analysis, Closing, Skeletonisation	Confocal microscopy	Vaa3D
ATLAS Vesicle segmentation method	1147	Object detection, Spot detection
FFmpeg	1144	Conversion
GDSC plugins	1141	Colocalisation analysis, Spot detection	Bioimage informatics	Fiji
Tubeness	1140	Image feature detection	Bioimage informatics	ImageJ
Reconstruct	1136	Filament tracing, Neuron image analysis	Scanning electron microscopy, Confocal microscopy
Adipocyte quantification ImageJ by Baecker	1134	Cell segmentation	Digital histology	ImageJ
Adipocyte quantification MATLAB	1132	Cell segmentation	Digital histology	MATLAB
JFilament	1133	Filament tracing, Active contours, Neuron image analysis		ImageJ
Directionality	1135			ImageJ
KNIME	1130
EBImage	1128	Image analysis, Image segmentation, Image processing, Geometrical transformation, Morphological operation	Bioimage informatics, High content screening	Bioconductor
Data-analysis strategies for image-based cell profiling	1129		High content screening
NET - Network Extraction Tool	1126	Filament tracing, Image thresholding, Shape features	Digital histology
ORION	1127	Filament tracing, Neuron image analysis, Image enhancement, Image deconvolution	Fluorescence microscopy, Confocal microscopy, Multi-photon microscopy
AVEMAP	1124	Image analysis, Wound-healing analysis, Optical flow analysis	Imaging, Fluorescence microscopy	Icy Matlab blocks
NeuronMetrics	1125	Filament tracing, Neuron image analysis, Shape features	Imaging
Hessian by Philippe Thévenaz	1122	Image enhancement		ImageJ
Laplacian by Philippe Thévenaz	1121	Image enhancement		ImageJ
Matlab compiler runtime	1117
gradient by Philippe Thévenaz	1119	Image enhancement	Imaging	ImageJ
Neural Circuit Tracer	1118	Filament tracing, Neuron image analysis, Image enhancement	Confocal microscopy, Multi-photon microscopy	Matlab compiler runtime
Microscopy Image Browser (MIB)	1079	Image segmentation, Image enhancement, Visualisation	Electron microscopy, Light microscopy
AnaMorf	1120	Filament tracing		ImageJ
Kappa	1074	Shape features	Digital histology	Fiji
iTrack4U	1073	Isolated object tracking	Light microscopy, Phase contrast microscopy	ImageJ, jMathPlot
ImageJ Analyze Skeleton	1072	Filament tracing, Pixel classification, Object detection		ImageJ, Analyze 12.0
MorphoGraphX	832	Image denoising	Confocal fluorescence microscopy
FigureJ	206	Visualisation, Montage	Data sharing	ImageJ
hIPNAT	69	Filament tracing, Neuron image analysis, Object feature extraction	Bioimage informatics	ImageJ
CIDRE	68	Illumination correction	High content screening, Light microscopy	ImageJ, MATLAB
wnd-charm	67	Image analysis, Shape features, Image feature detection, Analysis	Bioimage informatics, Machine learning
Rivulet	66	Filament tracing, Neuron image analysis	Confocal microscopy, Machine learning	MATLAB
TReMAP	65	Filament tracing, Image thresholding, Neuron image analysis	Confocal microscopy	Vaa3D
APP2	64	Filament tracing, Neuron image analysis, Distance transform	Confocal microscopy	Vaa3D
Vaa3D	62			3D Viewer, ICY Annotation, ITK, Vaa3D
APP (All-path pruning)	63	Filament tracing, Image thresholding, Neuron image analysis	Confocal microscopy	Vaa3D
QuimP	61	Cell segmentation, Interactive segmentation, Shape features, Object tracking, Cell tracking	Fluorescence microscopy
Scipion	58	Alignment construction, Image reconstruction, Tomographic reconstruction	Electron microscopy
Angiogenesis / Sprout Analyzer (ImageJ)	53	Filament tracing, Neuron image analysis	Bioimage informatics, Fluorescence microscopy	ImageJ
SOAX	52	Image analysis, Filament tracing, Active contours, Skeletonisation	Fluorescence microscopy, Confocal fluorescence microscopy	Active Contours
performing automatic registration for CLEM	50	Alignment construction, Image registration, Affine registration, Rigid registration, Spot detection	Correlative Light and Electron Microscopy
Spot Detector (Icy)	49	Spot detection, Image segmentation, Cell segmentation	Electron microscopy, Light microscopy, Bright field microscopy
WormGUIDES Atlas	1116	Analysis, Object feature extraction, Annotation, Visualisation	Bioimage informatics
JACoP	39	Object-based colocalisation, Object-based colocalisation, Pixel-based colocalisation, Colocalisation analysis, Colocalisation analysis	Fluorescence microscopy	ImageJ
ImageJ	38
Image Composite Editor	1115			Image Stitching
GelBandFitter	1114	Analysis	Imaging
Super-Resolution Radial Fluctuations (SRRF)	37	Image deconvolution, Image denoising	Super-resolution microscopy	ImageJ
Spotsizer	34		Bioimage informatics
CellProfiler	31
PopulationProfiler	1113		Statistics
BioImageXD	27	Image analysis, Image processing, Image visualisation
ADAPT	30	Analysis, Object detection	Fluorescence microscopy	ImageJ
Advanced Cell Classifier	26	Image analysis, Image classification, Image annotation, Image visualisation	Bioimage informatics, Machine learning	Matlab Image Processing Toolbox, Matlab compiler runtime
CellTrack	23	Cell tracking	Bioimage informatics
ImageJFX	18	Image analysis, Data handling	Bioimage informatics	Fiji
QuantCenter	1110	Analysis, Image classification, Cell segmentation, Object classification, Object detection, Pattern recognition, Visualisation	Bioimage informatics, Digital histology, Fixed sample imaging
ColorLab	1108	Image processing		MATLAB
Spine classification based on kernel density estimation	1107	Neuron image analysis, Classification		MATLAB, Matlab Image Processing Toolbox
simpleElastix	1105	Image registration, Affine registration, Rigid registration	Multimodal imaging
Local Phase Quantization (LPQ) descriptors	1104	Image feature detection, Image processing		MATLAB
ASAP	1103	Image annotation, Data handling, Image visualisation	Bioimage informatics
MyTardis	1102	Data handling	Data sharing
QuPath	1101	Cell segmentation, Interactive segmentation, Pixel classification, Annotation, Image annotation	Digital histology, Machine learning, Supervised learning
BSIF (Binarized Statistical Image Features)	1100	Image feature detection, Texture extraction, Image processing		Matlab Image Processing Toolbox, MATLAB
CBIRetrieval	1099
Local BInary Pattern (general code)	1095	Image feature detection, Image processing		MATLAB
matlabPyrTools	1093	Frequency analysis, Image feature detection, Image processing	Bioimage informatics	MATLAB, MATLAB Wavelet toolbox
muscleQNT: Muscle fiber counting	1092	Cell segmentation, Object counting, Shape features	Fluorescence microscopy	Mahotas, OpenCV, SciPy, PIL, NumPy, Python
Pyxit Landmark detection	1091	Landmark assignment	Bioimage informatics, Supervised learning	Cytomine
Neurolucida	1090	Cell segmentation, Neuron image analysis, Object feature extraction	Bioimage informatics, Confocal fluorescence microscopy, Structured illumination microscopy, Confocal microscopy, Bright field microscopy
SIMcheck	1089	Image analysis	Structured illumination microscopy	ImageJ
Pyxit segmentation model prediction	1088	Image classification, Image segmentation	Digital histology, Machine learning	Cytomine
Pyxit segmentation model builder	1087	Image segmentation, Pattern recognition	Digital histology, Machine learning	Cytomine
Colormine	1086	Conversion	Bioimage informatics
Pyxit object classification prediction	1084	Pattern recognition	Machine learning	Cytomine
Pyxit object classification model builder	1083	Object classification, Pattern recognition	Machine learning
SLDC (Segment Locate Dispatch Classify)	1082	Image feature detection, Cell segmentation	Machine learning	scikit-image, Cytomine, Segmentation of Clustered Cells in MATLAB
ec-clem autofinder	10	Image registration, Rigid registration, Affine registration	Correlative Light and Electron Microscopy
Icy Protocols	11	Data handling	Bioimage informatics	JavaDoc Parser, Icy Protocols SDK
eC-CLEM	9	Alignment construction, Image registration, Affine registration, Rigid registration, Deformable registration	Correlative Light and Electron Microscopy, Multimodal imaging
imageHTS	1081			Segmentation of Clustered Cells in MATLAB, ImageJ Feature Extraction
jicbioimage	165	Image analysis, Image processing	Bioimage informatics	Bio-Formats
TurtleSeg: 3D Image Segmentation Software	164	Interactive segmentation	Bioimage informatics
Huygens Remote Manager	161	Data handling	Bioimage informatics, Data sharing
IceImarisConnector	162			MATLAB, Imaris
XuvTools	163	Image reconstruction, Image stitching	Bioimage informatics, Confocal microscopy
InfectionCounter	313	Object counting	Imaging	ImageJ, Cell Counter ImageJ
NeurphologyJ	314			ImageJ
Analyze Particles	1070	Image feature detection	Microscopy	ImageJ, Fiji
Voronoi ImageJ	1071		Bioimage informatics	ImageJ
ViBE-Z	160	Image registration, Deformable registration	Bioimage informatics, Confocal fluorescence microscopy, Multimodal imaging
Auto-Bayes	159	Single molecule localisation	Single molecule localization microscopy, Statistics
SynPAnal	158	Object feature extraction	Confocal fluorescence microscopy
StabiTissue	1069	Rigid registration	Bioimage informatics	Python
PSF Lab	1068	Image generation	Fluorescence microscopy	PSF Generator
FOCAL	157
MIATool	156			Segmentation of Clustered Cells in MATLAB
WaveTracer	1067	Image reconstruction	Bioimage informatics	Metamorph
Clus-Doc	155
Distance Analysis (DiAna)	1066	Colocalisation analysis	Bioimage informatics	Fiji
2D-3D distributed parallel region competition segmentation	1064	Image segmentation	Bioimage informatics
MosaicSuite	1063	Filament tracing, Spot detection, Image segmentation, Particle tracking, Illumination correction, Visualisation	Imaging	Fiji, ImageJ 2.x
Balanced SOFI	154			MATLAB
Morpholeaf	1061	Image registration, Image feature detection	Bioimage informatics	FreeD
FreeD	153	Deformable registration, Feature-based registration, Image segmentation, Analysis, Clustering	Bioimage informatics	Segmentation of Clustered Cells in MATLAB
SuReSim	152		Single molecule localization microscopy
arivis Vision4D	151	Image analysis, Image annotation, Data handling, Image processing, Image visualisation	Bioimage informatics
3D segmentation (reconstruction) and modeling using Free-D	312	Image registration, Analysis, Image segmentation
ThunderSTORM	150	Image analysis, Visualisation	Bioimage informatics, Super-resolution microscopy	ImageJ
MicrobeJ	149	Analysis, Image thresholding, Object detection, Object tracking, Morphological operation	Bioimage informatics, Statistics	ImageJ
MultiStackReg	1059	Alignment construction, Image registration	Imaging, Electron microscopy, Light microscopy	Fiji, TurboReg
classification of hemp fibers based on morphological features	311	Watershed segmentation, Object classification, Image feature detection, Object feature extraction, Morphological operation	Microscopy	ImageJ, MATLAB, MorphoLibJ
SIMToolbox	148	Image reconstruction, Structured illumination reconstruction, Image processing	Structured illumination microscopy
fairSIM	147	Image reconstruction	Super-resolution microscopy, Structured illumination microscopy
Grayscale granulometry	1058	Morphological operation, Analysis	Microscopy
KNOSSOS - 3D image visualization and annotation tool	146	Image segmentation, Image annotation, Skeletonisation, Image visualisation	Bioimage informatics, Electron microscopy, Serial block-face scanning electron microscopy
MorphoLibJ	1057	Image segmentation, Cell segmentation, Watershed segmentation, Object counting, Object feature extraction, Shape features, Morphological operation	Bioimage informatics, Microscopy	ImageJ
Fourier Ring Correlation	1056	Frequency analysis, Image analysis	Bioimage informatics, Super-resolution microscopy	ImageJ
MorphoLibJ: using morphological reconstructions to isolate objects	310	Image segmentation, Morphological operation		ImageJ, MorphoLibJ
neuTube (or NeuTu)	145	Filament tracing, Neuron image analysis, Editing	Bioimage informatics	3D Viewer
BiDiFuse	1055	Alignment construction	Bioimage informatics
iterative closest point registration	1054	Rigid registration	Bioimage informatics
Hough Circles	1053	Image feature detection, Object feature extraction	Bioimage informatics	ImageJ
ABSnake	1052	Active contours	Bioimage informatics	ImageJ
Lama: The LocAlization Microscopy Analyzer	144	Colocalisation analysis, Cell segmentation	Single molecule localization microscopy
MosaicIA	1051	Colocalisation analysis, Image segmentation, Interactive segmentation, Particle tracking	Bioimage informatics	Fiji, MosaicSuite
SR-Tesseler	143	Analysis, Cell segmentation, Clustering	Super-resolution microscopy, Single molecule localization microscopy
AIR tools II	142	Image reconstruction	Bioimage informatics
Cytomine	141	Data handling, Image annotation	Data sharing, Digital histology
Labview	140
Skeletonize	1050	Object feature extraction, Morphological operation	Bioimage informatics	ImageJ
Angiogenesis Analyzer for ImageJ	309	Image analysis	Imaging	ImageJ
FibrilTool	308	Frequency analysis, Filament tracing, Interactive segmentation	Microscopy, Statistics	ImageJ
ImageJ Plugin LineageTracker	1049	Cell tracking	Bioimage informatics, Fluorescence microscopy	ImageJ
GDSC Single Molecule Localisation Microscopy	1048	Single molecule localisation	Bioimage informatics, Single molecule localization microscopy	ImageJ
OpenComet	307			ImageJ
FeatureJ Derivatives	1047	Image feature detection	Bioimage informatics	ImageJ
ImageJ Plugin Ridge Detection	1046	Image feature detection	Bioimage informatics	Fiji
ImageJ Plugin for Non-Local-Means Filtering	1045	Image denoising	Bioimage informatics	ImageJ
TANGO Tools for Analysis of Nuclear Genome Organization	1044	Image analysis, Image processing, Visualisation	Bioimage informatics, Fluorescence microscopy, Statistics
VolViewer	138			3D Viewer
Pandore	137	Image processing	Bioimage informatics
ISE-MeshTools	136
Adiposoft	1043	Cell segmentation, Image thresholding, Watershed segmentation	Digital histology	ImageJ
Find Maxima	1042	Image feature detection, Object feature extraction	Bioimage informatics	ImageJ
TransformJ	1041	Geometrical transformation, Affine transformation	Bioimage informatics	ImageJ
MTrackJ	1040	Object tracking		ImageJ, ImageScience.jar
FeatureJ Laplacian	1038	Image feature detection	Bioimage informatics	ImageJ
FindFoci	1037	Spot detection	Bioimage informatics	Spot Detection (KNIME)
SpotFinderM	1036	Spot detection, Cell tracking	Bioimage informatics, Fluorescence microscopy
SpotFinderZ	1035	Object tracking	Bioimage informatics	MATLAB
ImageJ Bandpass filter	1034	Frequency analysis, Image enhancement, Feature enhancement	Bioimage informatics	ImageJ
PRIISM/IVE	135
ICS tools	1033	Image analysis, Particle tracking, Optical flow analysis	Bioimage informatics, Fluctuation based microscopy, Fluorescence correlative spectroscopy	ImageJ
Microscope Image Correlation Spectroscopy MICS	1032	Object feature extraction, Collective object tracking	Image correlation spectroscopy	ImageJ
2D and 3D tracking based on global cost function optimization	306	Object tracking, Particle tracking, Trajectory analysis	Bioimage informatics, Machine learning	ImageJ, MTrackJ, ImageScience.jar, Jama, Tracking2.0
Root tools	305			ImageJ
SLOTH	304	Object tracking	Fluorescence microscopy	Python, matplotlib, NumPy, SciPy
HDF5 plugin for Fiji and ImageJ	303			ImageJ, Fiji
Visiopharm	134			Segmentation of Clustered Cells in MATLAB
Colony Blob Count Tool	302	Object counting	Bright field microscopy	ImageJ
PhenoRipper	133	Analysis, Image analysis, Object counting, Shape features, Data handling	Microscopy, Light microscopy
Kymoquant	301			ImageJ
DNA MicroArray Image Processing Case Study	300	Image segmentation, Spot detection		MATLAB, Matlab Image Processing Toolbox, MATLAB Signal Processing Toolbox
Correct 3D drift	1030	Image registration	Live sample imaging, Fluorescence microscopy, Confocal microscopy
MATLAB Image Segmentation Tutorial	299	Image segmentation		MATLAB, Matlab Image Processing Toolbox
MountainsMap	132			Segmentation of Clustered Cells in MATLAB, Spot Detection (KNIME), MountainsMap
Zebrafish Embryo Tool	298	Alignment construction	Fluorescence microscopy	ImageJ
Cell segmentation in phase contrast images	297	Cell segmentation, Active contours, Object tracking, Cell tracking	Phase contrast microscopy	MATLAB
Worm Toolbox: High.throughput screening of C. elegans	296			CellProfiler
idTracker: Tracking animals	295	Object tracking		MATLAB
Myotracker	294		Bright field microscopy	Fiji
3D affine transformation based on paired points	293	Affine transformation, Linear transformation		Fiji
Measure cell volume over time	292	Cell tracking		ImageJ, Imaris
Variational algorithms to remove stationary noise	1029	Image denoising	Microscopy
Tracing data using PALMsiever	291			PALMsiever
Generate animations from image data	290			Imaris, Imaris
CellSegm	131	Cell segmentation	Bioimage informatics	MATLAB
DBSCAN clustering using PALMsiever	289	Cell segmentation	Single molecule localization microscopy	PALMsiever
Drift correction using PALMsiever	288	Drift correction	Super-resolution microscopy	PALMsiever
Localization microscopy filtering using PALMsiever	287			PALMsiever
Segmentation of Clustered Cells in MATLAB	286	Cell segmentation, Watershed segmentation, Morphological operation	Fluorescence microscopy	MATLAB
Segmentation and quantification of subcellular structures in fluorescence microscopy images using Squassh	285	Image segmentation, Object-based colocalisation, Colocalisation analysis	Fluorescence microscopy	ImageJ, Squassh
FISH-quant	284	Spot detection	Bioimage informatics	Matlab Image Processing Toolbox, MATLAB, MATLAB Optimization toolbox, MATLAB Statistics toolbox
Intelligent Imaging	283	Data handling	High content screening	ImageJ
Register Virtual Stack Slices (ImageJ)	282	Image registration	Bioimage informatics	ImageJ
RapidSTORM	130	Image processing	Super-resolution microscopy, Single molecule localization microscopy
Evaluate spectral demixing measurement	281			MATLAB, RapidSTORM
PixFRET	280			ImageJ
CytooChip Analysis	279			ImageJ
Evaluate 3D data with a bead calibration sample	278		Single molecule localization microscopy	RapidSTORM
Measure Rosette Area Tool	277	Image thresholding	Bioimage informatics	ImageJ
Leaf Segmentation using Trainable Weka Segmentation plugin	276	Image segmentation	Machine learning	Fiji
Splitting clustered cells	275	Watershed segmentation		MATLAB, Graylevel Watershed for ImageJ
RapidSTORM usage tutorial	274	Single molecule localisation	Single molecule localization microscopy	RapidSTORM
FISHfinder	273	Spot detection		MATLAB
SGP-dec, A Scaled Gradient Projection method for 2D and 3D images deconvolution	272	Image deconvolution	Confocal fluorescence microscopy, Structured illumination microscopy	MATLAB, Matlab Image Processing Toolbox
MATLAB CellDetector	271	Cell segmentation	Digital histology, Fluorescence microscopy, Phase contrast microscopy, Machine learning	MATLAB, Matlab Image Processing Toolbox
Texture Analyzer (ImageJ)	1028	Image feature detection, Texture extraction	Bioimage informatics	ImageJ
3D intensity profile	270			Fiji
Focal Adhesion Analysis Server	269	Object tracking
2-D Colocalisation in Cells	268	Colocalisation analysis, Object-based colocalisation		CellProfiler, CellProfiler
Lymphatic Vessel Density calculation	267	Image segmentation	Digital histology	MATLAB, Pandore, Moment thresholding (ImageJ)
3D object based colocalization using KNIME	266	Object-based colocalisation, Colocalisation analysis		KNIME Image Processing and Analysis
Color normalization of H&E stains	265	Image deconvolution	Digital histology	MATLAB
Particle tracking with OMERO	264	Object tracking		OMERO, OMERO.matlab
2D tracking using KNIME and Fiji	262	Object tracking		KNIME Image Processing and Analysis, Fiji
ImmunoMembrane	259	Cell segmentation, Object classification	Digital histology	ImageJ
2D spots counting using KNIME	258	Spot detection		KNIME Image Processing and Analysis
Performing a Fluorescence Recovery after Photobleaching (FRAP) experiment	257		Confocal fluorescence microscopy	ImageJ, Excel
ICY batch pixel density measurement	256	Object feature extraction	Statistics
easyFRAP	129		Fluorescence microscopy
ICY Median filter via ImageJ	254	Image processing, Image convolution	Bioimage informatics
Magic Montage	253	Montage	Data sharing	ImageJ
Organise Image Data using OMERO	252			OMERO
Cell segmentation and quantification with CellX	250	Image segmentation, Cell tracking	Bright field microscopy, Phase contrast microscopy	Matlab Image Processing Toolbox, MATLAB
Find, Draw and Measure Wells in a Multi-Well Plate Picture	249	Image segmentation		ImageJ
OMERO.figure	248			OMERO
Manual Tracking Components of ImageJ	247	Object tracking		Fiji
scikit-image	128	Analysis, Image processing	Bioimage informatics
Separate image channel in folder	246
quickPALM	245			ImageJ, Micro-Manager
Moment thresholding (ImageJ)	1026	Image segmentation, Image thresholding	Bioimage informatics	ImageJ
2D cell tracking and analysis of morphological dynamics	244	Cell segmentation, Active contours, Cell tracking		ImageJ, QuimP
Image anonymisation	243			ImageJ
Track cell intensity	242	Active contours, Cell tracking
slideToolkit	241	Image segmentation, Image stitching	Digital histology	CellProfiler, OpenSlide, bftools, GNU Parallel, ImageMagick, Libtiff
Extract_Images	240			ImageJ, LOCI Bioformats plugin
Optical Flow	239			Optical Flow
LIF Projector	238	Image projection		ImageJ, Bio-Formats
Batch spot detection with custom output	237	Spot detection
LIF Extractor	236			ImageJ, Bio-Formats
OpenSlide	127	Image generation	Digital histology
Pixel Classification using ilastik	235	Image segmentation, Pixel classification, Image feature detection		VIGRA, ilastik
Counting foci in ImageJ	234			ImageJ
3D estimation of synaptic vesicle distribution in serial section TEM (ssTEM)	233
Ctrax - Caltech Multiple Fly Tracker	126
Automated velocity mapping of migrating cell populations (AVeMap)	232	Image segmentation, Object feature extraction	Bioimage informatics	MATLAB, Matlab compiler runtime
Uneven illumination correction	231	Illumination correction		CellProfiler, ImageJ
Wound healing assay: analysis in CellProfiler	230	Image segmentation, Wound-healing analysis		CellProfiler
CellProfiler Comet assay/DNA damage assay	228			CellProfiler
Leaf Infection Tools	227	Object-based colocalisation, Colocalisation analysis	Bioimage informatics	ImageJ, GDSC plugins
Oufti	226	Cell segmentation, Spot detection, Cell tracking	Fluorescence microscopy, Bright field microscopy	MATLAB
SparkMaster	225			ImageJ
Object Classification using ilastik	224	Image segmentation, Object classification		VIGRA, ilastik
Automatic 2D/3D Tracking using ilastik	223	Image segmentation, Object tracking	Bioimage informatics, Machine learning	ilastik
Measuring confluence in adherent cell cultures	222			ImageJ
Noise Suppression using Simple Spatial Filters	221	Image processing		ImageJ
Interactive Density Counting using ilastik	220			VIGRA, ilastik, ilastik
Artemia color analysis	219	Object feature extraction	Bioimage informatics	ImageJ
VSI File Extractor (ImageJ)	1025	Data handling	Bioimage informatics	Fiji
Human cytoplasm-nucleus translocation assay using CellProfiler	218		Bioimage informatics, Fluorescence microscopy	CellProfiler
Imaris Tracking	217			Imaris, Imaris
Measure distance of organelles from nucleus in 3D	216	Distance transform		Imaris, MATLAB
Find cells using nuclear and membrane fluorescence	215	Cell segmentation, Active contours
White Balance	214			ImageJ
Cells tracking in tissue	213			ImageJ, MATLAB, Graylevel Watershed for ImageJ
2D and 3D mitochondrial shape analysis and network properties	212	Analysis, Image segmentation	Confocal fluorescence microscopy	ImagePro
Object Tracking and Metadata Management	211	Cell tracking	Confocal microscopy	CellProfiler
Image denoising using Matlab	210	Image denoising	Bioimage informatics	MATLAB
Interactive Volume of Interest Extractor in Large 3D Stacks	209	Data handling	Bioimage informatics	ImageJ
Microtubule Length Analysis	208	Filament tracing, Image segmentation, Skeletonisation	Bioimage informatics, Fluorescence microscopy	Tubeness, Fiji
(Z,T,C) Stitcher	207	Image stitching	Microscopy	ImageJ
(Z,T) Hyperstack Stitcher	204	Alignment construction, Data handling, Image stitching	Bioimage informatics, Microscopy	ImageJ
Marker-controlled Watershed (ImageJ)	1024	Watershed segmentation, Morphological operation	Bioimage informatics	ImageJ
ImmunoRatio	203	Image deconvolution	Digital histology	ImageJ, Colour Deconvolution
Tube un-winder	202	Image projection		Fiji
SPIM de-striper	201	Image processing, Image correction	Light-sheet microscopy	Fiji
Morphological Segmentation (ImageJ)	1023	Watershed segmentation, Morphological operation	Bioimage informatics	ImageJ
Tracking of focal adhesions in 2D time lapse movies	200	Image segmentation, Object tracking		MATLAB
Tissue analysis from histological sections	199	Pixel classification	Digital histology, Machine learning	Fiji, Trainable Weka Segmentation
Quantifying staining in tissue sections	198	Spectral unmixing	Digital histology	ImageJ, Colour Deconvolution
Blood vessel segmentation and network analysis	197	Image segmentation	Light-sheet microscopy	Fiji
Volocity - 3D Object Segmentation and Tracking	196	Image feature detection, Object tracking		Volocity
Autofocus	195			ImageJ, Autofocus
KymographTracker	194	Object tracking	Fluorescence microscopy
Protein Micro-array Analysis	193	Image segmentation		Fiji
FISH signals detection	192	Spot detection		Fiji
Aphelion	125	Image analysis, Image processing	Bioimage informatics
CellProfiler Examples - Speckle Counting	191	Spot detection, Image segmentation	Bioimage informatics	CellProfiler
Quantitative analysis of focal adhesion dynamics	190	Particle tracking		MATLAB
CellProfiler Examples - Colocalization	189	Colocalisation analysis, Object-based colocalisation		CellProfiler
Microtubule end tracking in Drosophila Oocyte	188	Object tracking		Fiji, Bleach Correction, Fourier Bandpass Filter, Temporal Medial Filter, TrackMate
Quantitative analysis of focal adhesions	187	Image segmentation, Image thresholding	Fluorescence microscopy	ImageJ, Log3D, CLAHE
3D cell tracking and quantification of shape changes	186	Cell tracking		MATLAB
Multi Kymograph	185			ImageJ
spot detection and codistribution analysis	184	Colocalisation analysis, Object-based colocalisation, Spot detection, Object detection		ImageJ, MATLAB
Tissue Cell Segmentation	183	Image segmentation, Watershed segmentation	Fluorescence microscopy	ImageJ
Blob segmentation	182	Image segmentation		Fiji, MorphoLibJ
Wound healing assay: analysis in ImageJ	181	Image segmentation, Wound-healing analysis		ImageJ
ActionBar (ImageJ)	1022	Data handling		ImageJ
Analyzing gels and western blots with ImageJ	179			ImageJ
plusTipTracker	178	Object tracking	Statistics	MATLAB, Matlab Image Processing Toolbox, MATLAB Curve Fitting Toolbox, MATLAB Statistics toolbox, MATLAB Optimization toolbox
FLIM / SLIM Analysis	177			ImageJ
python-bioformats	124
python-javabridge	123
ijblob	1021	Object detection, Object feature extraction, Shape features	Bioimage informatics	ImageJ
Counting Clumped Cells	175	Cell segmentation, Object counting		ImageJ
Histo_surfaces	174		Digital histology	ImageJ
Centromere Recognition and Quantification	173	Spot detection	Fluorescence microscopy	ImageJ, Spot Detection (KNIME)
Orthogonal Views (ImageJ)	1020	Image visualisation	Bioimage informatics	ImageJ
v3dlib	121
softWoRx 5.0	120
SimuCell	119			MATLAB
ImagePro	118
ITK-SNAP	117	Image segmentation, Interactive segmentation, Active contours, Image annotation	Imaging, Multimodal imaging
Micro-Manager	116			ImageJ
Metamorph	115
Huygens	114	Colocalisation analysis, Object-based colocalisation, Single molecule localisation, Object tracking, Image deconvolution, Chromatic aberration correction, Image visualisation, Volume rendering	Light-sheet microscopy, Widefield microscopy, Fluorescence microscopy, Confocal fluorescence microscopy, Super-resolution microscopy
GNU Octave	113			MATLAB
CATMAID	112	Image segmentation, Interactive segmentation, Image annotation, Data handling, Visualisation, Image visualisation	Data sharing, Electron microscopy, Light-sheet microscopy
Avizo	111
AutoQuant	110	Image deconvolution	Fluorescence microscopy
Amira	109	Image registration, Analysis, Visualisation	Multimodal imaging
OpenCV	108			Object Tracking and Metadata Management
OpenMOLE	107
Volocity	105			3D Viewer
Find Focused Slices	1019	Image feature detection, Image validation	Bioimage informatics	ImageJ
NeuronStudio	104	Filament tracing, Neuron image analysis, Skeletonisation	Confocal microscopy
Microtubules Tool (3D)	172	Filament tracing, Image thresholding	Bioimage informatics	ImageJ, Fiji, Skeletonize3D, 3D Objects Counter
Arabidopsis Seedlings Tool	171	Image thresholding	Bioimage informatics	ImageJ
Cell segmentation by EBImage, R	170			Graylevel Watershed for ImageJ, Segmentation of Clustered Cells in MATLAB
pythonxy	103	Analysis, Visualisation		Python
IMOD	102	Alignment construction, Image analysis	Electron microscopy, Multimodal imaging
MATLAB	101			ImageJ Feature Extraction, Connected Components
Golgi Segmentation by Active Mask framework	169	Cell segmentation		Matlab Image Processing Toolbox, ImageJ
Aquiarium	100	Image segmentation, Image correction, Chromatic aberration correction	Fluorescence microscopy
Columbus Image Data Storage and Analysis System	99
3D Slicer	98			3D Viewer, ITK
Endrov	97			ICY Annotation, OMERO, Processing, ImgLib2, ImgLib2
Bio7	96			ImageJ
Manual Frame Drift Registration	168	Image registration, Drift correction, Image correction	Fluorescence microscopy	ImageJ, Manual Tracking ImageJ
ImageJ 2.x	94
u-track	93	Affine registration, Cell tracking, Particle tracking, Visualisation	Microscopy, Fluorescence lifetime imaging microscopy	Matlab Image Processing Toolbox, Bio-Formats
Cell segmentation and measurements	167			CellProfiler, Segmentation of Clustered Cells in MATLAB
ITK	92	Image registration, Image analysis, Image segmentation, Image thresholding
Schnitzcells	91			MATLAB
Matlab Computer Vision System Toolbox	90			MATLAB, Optical Flow, Object Tracking and Metadata Management
Matlab Image Processing Toolbox	89			MATLAB
ilastik	88	Image segmentation, Object classification, Object counting, Object feature extraction, Object tracking, Image annotation	Bioimage informatics, Digital histology, In-silico reconstruction, Machine learning	VIGRA
Imaris	87	Image registration, Object detection, Object tracking, Visualisation	Multimodal imaging	Imaris
Mahotas	85	Image classification, Image thresholding, Watershed segmentation, Shape features, Morphological operation, Image processing		Python, NumPy
FARSIGHT	84			Segmentation of Clustered Cells in MATLAB
Definiens Developer	83
Icy	82
ImgLib2	80		Bioimage informatics	ImageJ
Fiji	79
OMERO	77	Data handling, Image annotation	Bioimage informatics, Data sharing	OMERO
PALMsiever	76	Visualisation	Super-resolution microscopy	MATLAB, Histogram
PSF Tool 2D	960	Image generation	Bioimage informatics, Fluorescence microscopy	ImageJ
3D PSF estimator	961	Image feature detection	Fluorescence microscopy	ImageJ, Fiji, MosaicSuite
Particle Tracker 2D/3D	962	Object tracking, Particle tracking	Live sample imaging, Fluorescence microscopy	Fiji, MosaicSuite
Region Competition	964	Image segmentation, Cell segmentation	Imaging, Fluorescence microscopy	Fiji, MosaicSuite
Squassh	965	Colocalisation analysis, Object-based colocalisation, Cell segmentation	Fluorescence microscopy	Fiji, MosaicSuite
affine (EBImage)	967	Affine transformation	Bioimage informatics	EBImage
EBImage blackTopHat	968	Morphological operation	Bioimage informatics	EBImage
EBImage bwlabel	969	Object counting	Bioimage informatics	EBImage
EBImage channel	970	Data handling, Conversion	Bioimage informatics	EBImage rgbImage
EBImage closing	971	Morphological operation	Bioimage informatics	EBImage
combine (EBImage)	973	Data handling, Image generation	Bioimage informatics	EBImage
EBImage computeFeatures	974	Object feature extraction, Texture extraction	Bioimage informatics	EBImage
EBImage dilate	975	Morphological operation	Bioimage informatics	EBImage
EBImage display	977	Image visualisation		EBImage
EBImage distmap	978	Distance transform	Bioimage informatics	EBImage
EBImage erode	979	Morphological operation	Bioimage informatics	EBImage
erodeGreyScale	980			Morphological Operations
EBImage fillHull	981	Image correction	Bioimage informatics	EBImage
EBImage filter2	982	Frequency analysis, Image convolution	Bioimage informatics	EBImage
flip (EBImage)	983	Image generation, Geometrical transformation	Bioimage informatics	EBImage
floodFill	984	Image annotation	Bioimage informatics	EBImage
EBImage flop	985	Image generation	Bioimage informatics	EBImage
EBImage gblur	986	Smoothing	Bioimage informatics	EBImage
graph cut library	987	Image segmentation	Machine learning
ilastik - Automatic Tracking	988	Object tracking	Bioimage informatics, Supervised learning	ilastik
ilastik - Carving	989	Image segmentation, Interactive segmentation, Watershed segmentation, Object detection	Bioimage informatics, Machine learning	ilastik
ilastik - Density Counting	990	Spot detection, Object counting	Bioimage informatics, Machine learning	ilastik
ilastik - Manual Tracking	991	Object tracking	Bioimage informatics	ilastik
localCurvature	994	Image feature detection	Microscopy	R
EBImage makeBrush	995	Annotation	Bioimage informatics	EBImage
EBImage medianFilter	996	Smoothing	Bioimage informatics	EBImage
EBImage ocontour	997	Object feature extraction	Bioimage informatics	EBImage
EBImage opening	998	Morphological operation	Bioimage informatics	EBImage
EBImage paintObjects	1001	Object detection, Visualisation	Bioimage informatics	EBImage
readImage (EBImage)	1003	Data handling	Bioimage informatics	EBImage
Resize in EBImage	1004	Linear transformation	Bioimage informatics
restoreTools	1005	Image reconstruction, Image deconvolution, Image correction	Bioimage informatics	MATLAB
EBImage rgbImage	1006	Image generation	Bioimage informatics	EBImage
EBImage rmObjects	1007	Image generation	Bioimage informatics	EBImage
EBImage rotate	1008	Geometrical transformation	Bioimage informatics	EBImage
EBImage selfComplementaryTopHat	1009	Morphological operation	Bioimage informatics	EBImage
EBImage stackObjects	1010	Object classification, Image generation	Bioimage informatics	EBImage
EBImage thresh	1011	Adaptative thresholding	Bioimage informatics	Adaptive Thresholding (EBImage)
EBImage tile	1012	Data handling	Bioimage informatics	EBImage
EBImage translate	1013	Geometrical transformation	Bioimage informatics	EBImage
EBImage transpose	1014	Geometrical transformation	Bioimage informatics	EBImage
untile (EBImage)	1015	Data handling	Bioimage informatics	EBImage
EBImage writeImage	1018	Data handling	Bioimage informatics	EBImage
Background Subtractor	925	Image correction, Illumination correction	Fluorescence microscopy	Fiji, MosaicSuite
CellTracker	926	Object tracking, Cell tracking	Live sample imaging, Fluorescence microscopy
Convolve with 2D Bessel function	927	Synthetic image generation, Image convolution	Bioimage informatics, Imaging	ImageJ
CytoPacq	928	Synthetic image generation	Bioimage informatics, Data sharing
OMERO FLIMfit	930			OMERO
FishQuant	931
ImarisReader for MATLAB	934	Conversion		Imaris, MATLAB
ImarisImageProcessing	935			Invert (Icy), EBImage rotate, flip (EBImage), CellProfiler Crop, EBImage Median Filter, EBImage Median Filter, EBImage Median Filter, Histogram Equalization
ImarisSectionView	936
ImarisSliceView	937
Insert Poisson noise	938	Synthetic image generation	Imaging
Interaction Analysis	939	Image segmentation, Object detection	Fluorescence microscopy	Fiji, MosaicSuite
MATLAB/ Qu	940	Image analysis, Image processing, Visualisation	Bioimage informatics	MATLAB
Mahotas / Convolution	941	Image convolution	Bioimage informatics	Mahotas
Mahotas / Distance Transform	942	Distance transform	Bioimage informatics	Mahotas
Mahotas / Feature Computation	943	Image feature detection	Bioimage informatics	Mahotas
Mahotas / Imread	944	Data handling	Bioimage informatics	Mahotas
Mahotas / Labeled image manipulation	945	Object classification	Bioimage informatics	Mahotas
Mahotas / Morphological Operators	946	Morphological operation	Bioimage informatics	Mahotas
Mahotas / Multidimensional interpolation	947
Mahotas / SURF	948	Image feature detection	Bioimage informatics	Mahotas
Mahotas / Thresholding	949	Image thresholding	Bioimage informatics	Mahotas
Mahotas / Wavelets	950	Image reconstruction, Image convolution	Bioimage informatics	Mahotas
OMERO.editor	951	Editing	Data sharing	OMERO
OMERO.insight client	952			OMERO
OMERO.insight-ij client	953			ImageJ, OMERO
OMERO.matlab	954			MATLAB, OMERO
OMERO.searcher	955			OMERO
OMERO.server	956
OMERO.web client	957	Data handling	Bioimage informatics, Data sharing	OMERO
OMERO.webtagging	958	Annotation	Bioimage informatics	OMERO.web client
CellProfiler Align	923	Rigid registration		CellProfiler
CellCognition	75			Segmentation of Clustered Cells in MATLAB, ICY Annotation
WIS-PhagoTracker	74	Image segmentation, Object tracking	Bioimage informatics	MATLAB
VIGRA	73	Texture extraction, Classification, Geometrical transformation, Image convolution, Morphological operation	Bioimage informatics, Machine learning
WIS-NeuroMath	72	Image segmentation		MATLAB
Interactive Affine	916	Affine transformation		Fiji
3D Area	917			Processing
Interactive Perspective	918	Warping	Bioimage informatics	ImageJ
ImarisXT	919		Bioimage informatics, Data sharing	ImageJ, Imaris, MATLAB, ImarisCell, ImarisMeasurementPro, ImarisTrack, ImarisFilamentTracer, Python
Maximum Entropy Threshold (ImageJ)	920	Image segmentation, Image thresholding	Bioimage informatics	ImageJ
EnhanceEdges	921	Image correction, Contrast enhancement	Bioimage informatics	CellProfiler
MeasureObjectSizeShape (CellProfiler)	922	Object feature extraction, Shape features	Bioimage informatics	CellProfiler
Feature Calculation (KNIME)	775	Image feature detection, Image segmentation, Object feature extraction	Bioimage informatics	KNIME Image Processing and Analysis
Extract Images From PDF	776	Data handling		ImageJ
ExportToDatabase	777			CellProfiler
SIOX: Simple Interactive Object Extraction	778	Interactive segmentation	Bioimage informatics	ImageJ
RodCellJ	779	Cell segmentation, Cell tracking	Bioimage informatics, Fluorescence microscopy	ImageJ
Icy HK-Means	780	Image analysis, Image classification, Image segmentation, Object detection	Bioimage informatics, Fluorescence microscopy	Icy Thresholder, Spot detection utilities, Connected Components, EzPlug SDK, Filter Toolbox (Icy), Icy Protocols SDK
mcib3d library	781	Image analysis, Image segmentation, Annotation, Data handling, Image enhancement, Morphological operation	Bioimage informatics	Icy MereoTopology
Microscope Live 3D (deprecated)	782			Micro-Manager
Grid	783	Annotation, Image annotation	Microscopy	ImageJ, Grid
Local Thickness (ImageJ)	784	Object feature extraction, Shape features	Bioimage informatics	ImageJ
Delayed Snapshot	785		Bioimage informatics	ImageJ, Fiji
Feature Detector	786			Edge Detection, EzPlug SDK, Icy Protocols SDK
Histogram Equalization	787	Image processing, Image enhancement	Bioimage informatics, Imaging	Icy
Import ROI from ImageJ