Overview

GIANI is a FIJI plugin designed to facilitate routine analysis of 3D cell biology images. Implemented specifically with batch-processing in mind, GIANI is designed to:

• Read data sets in their native, proprietary format
• Automatically segment nuclei and cells
• Measure nuclear and cell morphology, together with fluorescence intensities within these regions.
• Allow users to explore their results

Segment Nuclei and Cells

Nuclei locations are estimated using blob detection…

…before full segmentation is achieved using a watershed operation…

…and then cells are similarly segmented:

Obtain Measurements

A complete set of morphological and intensity descriptors, across an unlimited number of channels, can then be obtained from the above segmentations.

Further Segmentation

If you wish, you can segment smaller, sub-cellular structures using additional blob detection:

Explore Results

Examine your results using the included results browser:

Want To Learn More?

See the Wiki for installation instructions and full documentation.

Citing GIANI

Please cite the following publication if you use GIANI in your work:

David J. Barry, Claudia Gerri, Donald M. Bell, Rocco D’Antuono, Kathy K. Niakan; GIANI – open-source software for automated analysis of 3D microscopy images. J Cell Sci 15 May 2022; 135 (10): jcs259511. doi: https://doi.org/10.1242/jcs.259511