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Following are some tools which are used for bio image analysis

Capabilities of different tools :

1. ImageJ2 and Icy, which are designed to handle a very wide range of applications.
2. CellProfiler and KNIME, especially for high-throughput analysis and data mining.
3. ilastik, especially when its powerful machine learning features are needed to identify or classify challenging structures.
4. QuPath, especially for digital pathology or whole slide image analysis.

– Source

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• Fiji
• 3DImageJSuite
• CellProfiler
• QuPath
• TrackMate