list of software

identifier has function has topic Requires

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 Keras, Tensorflow

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 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 Keras, Tensorflow, 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

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 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 Deformable registration Bioimage informatics, Confocal fluorescence microscopy

Auto-Bayes

159 Single molecule localisation Single molecule localization microscopy, Statistics

SynPAnal

158 Object feature extraction Confocal fluorescence microscopy

StabiTissue

1069 Rigid registration