list of software

	identifier	has function	has topic	Requires
webKnossos	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
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	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
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
Nuclei Tracking (TrackMate)	1613	Particle tracking		TrackMate, pyimagej
Particle Tracking (ImageJ)	1611	Particle tracking		ImageJ, FeatureJ Laplacian
Nuclei Segmentation 3D (Ilastik)	1610	Pixel classification	Machine learning	ilastik
Nuclei Segmentation 3D watershed (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	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	1568
ImageJFIJI	1566
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
Nuclei Segmentation (ilastik)	1488	Pixel classification	Machine learning	ilastik, scipy, numpy, scikit-image
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: Benchmark on Image Registration methods with Landmark validation	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
NanoJ	1443	Image analysis, Image processing	Fluorescence microscopy, Super-resolution microscopy	ImageJ
HAWK	1442	Image processing, Image correction	Fluorescence microscopy, Super-resolution microscopy	ImageJ
Nuclei Segmentation 3D DT Watershed (ImageJ)	1441	Image segmentation, Watershed segmentation, Smoothing		ImageJ
3D ImageJ Suite	1440	Colocalisation analysis, Image segmentation, Morphological operation		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
clij - GPU-acceleration for ImageJ	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		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			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
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
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
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	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
cython	1348
Rivulet 2 (Rivuletpy)	1349	Filament tracing, Image thresholding, Neuron image analysis, Distance transform		scipy, numpy, Python, Libtiff, simpleITK, cython
ZEN Blue	1345
ZEN Intellesis Trainable Segmentation	1346	Image segmentation, Image feature detection	Digital histology, High content screening, Electron microscopy, Light microscopy, Fluorescence microscopy, Machine learning	ZEN Blue
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
Chainer	1324			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
MATLAB Signal Processing Toolbox	1318
matplotlib	1317
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
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	Object counting, Spot detection	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 denoising, Image deconvolution	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
PIL	1287
numpy	1288
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	Multimodal imaging
Cancer Imaging Phenomics Toolkit (CaPTk)	1277
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
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	Fiji, CMTK
Z-spacing correction for Fiji	1204	Warping, Image correction	Electron microscopy	Fiji
Tensorflow	1201	Image classification, Image segmentation, Image enhancement, Image feature detection	Machine learning
Keras	1202
Isotropic Super-Resolution for EM	1203	Image enhancement	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, 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
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, Smoothing, Morphological operation, Skeletonisation, Image processing	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
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 segmentation, 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, Optical flow analysis	Topic, 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	Topic
AnaMorf	1120	Filament tracing		ImageJ
Kappa	1074	Shape features	Digital histology	Fiji
iTrack4U	1073	Isolated object tracking	Light microscopy, Phase contrast microscopy	ImageJ, jMathPlot
AnalyzeSkeleton	1072	Filament tracing, Object detection, Pixel classification		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	MATLAB, ImageJ
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	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	1116			3D Viewer
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			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
QuantCenter	1110		Bioimage informatics, Digital histology
ColorLab	1108	Image processing		MATLAB
Spine classification based on kernel density estimation	1107	Neuron image analysis, Classification		MATLAB, Matlab Image Processing Toolbox
simpleElastix	1105	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	scipy, PIL, numpy, Mahotas, OpenCV
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	Cytomine
SLDC (Segment Locate Dispatch Classify)	1082	Cell segmentation, Image feature detection	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	Affine registration, Deformable registration	Correlative Light and Electron Microscopy, Multimodal imaging
imageHTS	1081