- Developed for: Céline
- Team: Espeli
- Date: January 2023
- Software: Fiji
3D images taken with a x60 objective
2 channels:
- DAPI: DNA
- TL phase: bacteria
- Detect bacteria on the average intensity Z-projection of channel 2 with Omnipose
- Detect DNA on the average intensity Z-projection of channel 1 with Omnipose
- In each bacterium, return distances between bacterium centroid and DNA centroid
- 3DImageSuite Fiji plugin
- CLIJ Fiji plugin
- Omnipose conda environment + bact_phase_omnitorch_0 and bact_fluor_omnitorch_0 models
Version 1 released on January 5, 2023.
Version 2 released on July 4, 2023: can handle images with multiple series and times.