This repo contains a set of scripts developed by CAMDU to help automate quality control tasks on our microscopes.
auto_PSF.py - Just download it and run inside Fiji. It will look for files containing the string "psf" on their filenames and run for the number of beads required on those. The output is "summary_psf.csv" with one line per bead containing X/Y/Z resolution in um.
auto_FOV.py - Just download it and run inside Fiji. It will look for files containing the string "fov" on their filenames and run on those, with one line output for each file. The output is "summary_fov.csv" with one line per FOV image, containing the relative intensity of the dimmest corner compared to the centre.
auto_coloc.py - Just download it and run inside Fiji. It will look for files containing the string "coloc" on their filenames and run on those. The output is "summary_coloc.csv", with one line output for each file and bead containing the distance between channels. WARNING: this will not work if there are any spaces on your directory structure where the images are!
auto_stagerepro.py - Just download it and run inside Fiji. It will look for files containing the string "stage" on their filenames and run on those. The output is "summary_stagerepro.csv", with one line output for each file containing the maximum drift over the timelapse.
auto_PSF.py, auto_FOV.py, auto_coloc.py - requires MetroloJ installed with the iText library v.2.1.4. Newest Fiji version is always recommended.
auto_stagerepro.py - requires TrackMate, which should be available through Fiji.
Feel free to copy, remix, submit pull requests and so on!
- Erick Martins Ratamero - Scripting
- Claire Mitchell - Experimental input, workflow
This project is licensed under the MIT License - see the LICENSE.md file for details