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Name Category Image requires Type interaction level License/Openness has function has topic
BIIGLE Software BIIGLE Logo Collection Manual, Semi-automated Free and open source Object detection, Image annotation, Classification Bioimage informatics, Microscopy, Machine learning
HistoMetriX Software HistoMetriX for image analysis of histology slides Component, Workflow Commercial
TissUUmaps Software Collection Manual, Semi-automated Free and open source Visualisation, Image visualisation Bioimage informatics, Data sharing, Digital histology, Imaging
3D segmentation of cells based on 2D Cellpose and CellStitch Software example of usage Workflow Automated Free and open source Cell segmentation Fluorescence microscopy
CellStitch Software cellstitch Python Component Automated Free and open source Cell segmentation, Cell tracking, Image reconstruction Microscopy, Electron microscopy, Fluorescence microscopy
Proxywave Software need a thumbnail Collection
SegMetrics Software Python Component Automated Free and open source Validation Bioimage informatics
SuperDSM Software Python Collection Automated Free and open source Cell segmentation, Model-based segmentation Bioimage informatics
nanoFeatures Software GUI first tab to browse and input files, select input type and check extra filters if needed. Matlab Image Processing Toolbox, Matlab Computer Vision System Toolbox, MATLAB Component Semi-automated Free and open source Operation, Analysis, Image analysis, Image feature detection, Single molecule localisation, Object feature extraction, Shape features, Clustering Bioimage informatics, Imaging, Microscopy, Super-resolution microscopy, Single molecule localization microscopy, Machine learning, Unsupervised learning
ImageJ Binary Operations Software need a thumbnail ImageJ Collection Automated Free and open source Morphological operation Bioimage informatics
ELEPHANT Software from https://elephant-track.github.io/#/v0.5/?id=_5-proofreading Collection Semi-automated Free and open source Object detection, Cell tracking, Trajectory analysis, Visualisation Bioimage informatics, Live sample imaging, Light-sheet microscopy, Confocal fluorescence microscopy, Machine learning
ZeroCostDL4Mic Software need a thumbnail Collection Semi-automated Free and open source Image segmentation, Object detection, Image denoising, Image correction Electron microscopy, Super-resolution microscopy, Bright field microscopy, Machine learning
BiaPy: Bioimage analysis pipelines in Python Software need a thumbnail Python Collection Manual Free and open source Image classification, Image segmentation, Cell segmentation, Object detection, Image denoising Electron microscopy, Machine learning
Bayesian Tracker (btrack) Software need a thumbnail Python Collection Manual, Semi-automated Free and open source Analysis, Cell segmentation, Cell tracking Live sample imaging, Fluorescence microscopy, Machine learning
SLEAP Software Tensorflow, NumPy, Python Collection Semi-automated Free and open source Object tracking Machine learning
idtracker.ai Software OpenCV / CUDA, Python, PyTorch Collection Automated Free and open source Object tracking Machine learning
DAMAN Software daman PyTorch Component Automated Free and open source Cell segmentation Fluorescence microscopy, Bright field microscopy, Machine learning
Segmentation and Tracking of Mammary Epithelial Organoids in Brightfield Microscopy Software Adapted from https://cbia.fi.muni.cz/research/spatiotemporal/organoids.html ImageJ Workflow Semi-automated Free and open source Cell segmentation, Cell tracking, Synthetic image generation Live sample imaging, Bright field microscopy, Machine learning
OrganoSeg Software Figure 2 in OrganoSeg Scientific Reports publication Matlab Image Processing Toolbox Collection Semi-automated Free and open source Cell segmentation, Object feature extraction Bright field microscopy, DIC microscopy, Phase contrast microscopy
OrganoID Software need a thumbnail Python Collection Manual, Semi-automated Free and open source Cell segmentation, Object feature extraction, Object tracking Live sample imaging, Bright field microscopy, Phase contrast microscopy, Machine learning