orion-cirb / Cadherin_Junctions

Cadherin_Junctions

• Developed for: Gaëtan & Alexandre
• Team: Germain
• Date: April 2023
• Software: Fiji

Images description

3D images taken with a x63 objective on a widefield microscope

2 channels:

1. EGFP: Cadherin junctions
2. DAPI: Nuclei

Macros description

• Step 1: preprocessing.ijm:

  • DAPI channel: sum Z-projection + Otsu thresholding + median filtering + watersheding
  • EGFP channel: find focused slices + max z-projection

• 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

• 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 history

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.