- Developed for: Gaëtan & Alexandre
- Team: Germain
- Date: April 2023
- Software: Fiji
3D images taken with a x63 objective on a widefield microscope
2 channels:
- EGFP: Cadherin junctions
- DAPI: Nuclei
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Step 1: preprocessing.ijm:
- DAPI channel: sum Z-projection + Otsu thresholding + median filtering + watersheding
- EGFP channel: find focused slices + max z-projection
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Step 2: use ilastik to train a pixel classifier that can segment the EGFP channel image in 4 different classes: thin, finger, reticular and background
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Step 3: postprocessing.ijm or postprocessing_grid.ijm + draw_grid.ijm:
- DAPI channel: count the number of nuclei
- EGFP channel: measure the area of the 4 different classes (in the entire image or in each 64x64 pixels2 cell of a grid)
Version 1 released on April 26, 2023.
Version 2 released on May 10, 2023: postprocessing_v2.ijm or postprocessing_v2_grid.ijm.
Measure the area of the 5 different classes (in the entire image or in each 64x64 pixels2 cell of a grid): thin, finger, reticular, finger-reticular and background.
Version 3 released on June 8, 2023.
preprocessing.ijm: channels corresponding to nuclei and junctions asked in a dialog box.
postprocessing.ijm or postprocessing_grid.ijm: number of junctions classes asked in a dialog box.