microscopy-analysis

Description of each script

This file does particle detection that can be customized for each channel. Then is outputs either a csv or a txt file of the Results created by running the ComDet pluggin from FIJI and saves the results in a folder.
Make sure to open the results and identify how many columns there are since it is important for the Analysis_with_seg_user code

This file will use the output of the segmentation done by Cellpose to be able to give us the Integrated intensity of each cell for images and then outputs a result file as csv format for each image.

Name		Name	Last commit message	Last commit date
.DS_Store		.DS_Store
Analysis_with_seg_user.ipynb		Analysis_with_seg_user.ipynb
README.md		README.md
particle_detection_thereal.ijm		particle_detection_thereal.ijm
script_intensity.py		script_intensity.py