orion-cirb / Lamin_ORF1P

Lamin_ORF1P

• Developed for: Sandra
• Team: Fuchs
• Date: February 2023
• Software: Fiji

Images description

3D images taken with a x25 objective

3 channels:

1. 405: Nuclei
2. 488: Lamin (not mandatory)
3. 561: ORF1P

Plugin description

• Detect nuclei with Cellpose
• Compute nuclei 3D shape descriptors
• In lamin channel (if provided), measure nuclei intensity
• In ORF1P channel, get cytoplasm using a Gaussian filter + Moments thresholding + nuclei subtraction
• In ORF1P channel, measure nuclei and cytoplasm intensity

Dependencies

• 3DImageSuite Fiji plugin
• CLIJ Fiji plugin
• Omnipose conda environment + cyto2 model

Version history

Version 1 released on February 16, 2023.