SRS Worms

Package for processing and analysing multi-channel SRS worm images.

Requirements

Please see the requirements.txt file for the required packages. You can install them using the following command:

pip install -r requirements.txt

Also, a dedicated ImageJ installation is required for the stitching of the images.

Data folder structure

There should be invididual experiment folders. For simplicity, it is recommended that all experiment folders are managed under the same project folder:

project_folder
    ├── experiment_1
    ├── experiment_2
    ...

Each experiment folder should look like this:

experiment_folder
    ├── calibration_fnorm.tif
    ├── image_subfolder_1
    |   ├── worm_image_with_desc_1.tif
    |   ├── worm_image_with_desc_2.tif
    |   ...
    ├── image_subfolder_2
    ...

The files include:

• calibration_fnorm.tif: the calibration image taken for field normalisation
• worm_image_with_desc_1.tif: the worm image with a description of the worm (e.g. treatment, timepoint, imaging parameters, etc.). For example, it can be

AD01_vit1mCherry_vit2GFP_300gain_10pbf_Zoom1_20240617_plate1_worm1_1x7.tif

Usage

TBD.