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Cell Counter is an ImageJ plugin for manually marking and counting cells or other objects in microscopy images. It is intended for researchers who need a lightweight counting workflow with multiple marker types and saved annotations.
💡 Pick it when you need automated, repeatable cell counting across many images.
CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from...
💡 Choose it for tissue sections, whole-slide images, and richer cell classification.
QuPath is a powerful open-source digital pathology solution designed to meet the needs of professional pathologists and researchers.
ilastik developers
💡 Pick it when you want interactive machine-learning segmentation without building a code-heavy pipeline.
ilastik is a free interactive machine-learning toolkit for segmenting and classifying biological images. It is aimed at researchers who want to train...
Oxford Instruments
💡 Choose it for advanced 3D, 4D, and time-lapse cell tracking with commercial support.
Imaris is commercial 2D, 3D, and 4D microscopy analysis software for researchers analyzing cells, tissues, and volumetric datasets. Its standout capability is...
Media Cybernetics
💡 Pick it for supported, configurable microscopy measurement and reporting in commercial labs.
Image-Pro is commercial image-analysis software for laboratories that need measurement, segmentation, and reporting across microscopy and scientific images. It stands out with...
MIPAR Software
💡 Choose it when you need customizable automated segmentation and batch quantification for difficult images.
MIPAR is commercial software for automated image segmentation, measurement, and analysis of microscopy and materials-science images. It is designed for users who...
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