Crunch the data

The first step is to get the data from the microscope into usable form. This is done by iss project-and-average. This script will project the data into a single image and average the data across rounds and channels to generate illumination correction images. It will also generate ROI overviews that can be used to select the reference tiles.

Overview

The command is run as follows:

iss project-and-average --path relative/path/to/data

By default, the script will process only new files. There is a --force-redo flag that will force the script to re-run all steps, even if the output files already exist.

Details

The script will perform the following steps:

        ---
 config:
 look: classic
 layout: dagre
 ---
 flowchart TD
 subgraph Projecting["Projecting"]
         prj((("project_round")))
         find["Find acquisitions"]
         check["check_roi_dims"]
         reprj["reproject_failed"]
 end
 subgraph Averaging["Averaging"]
         s_av["create_all_single_averages"]
         g_av["create_grand_averages"]
 end
 subgraph subGraph2["ROI overview"]
         ovw(["plot_overview_images"])
 end
 subgraph subGraph3["Project and average"]
         Projecting
         Averaging
         subGraph2
 end
     start["Start"] --> find
     find --> prj
     prj --> check & s_av
     check --> reprj
     reprj --> prj
     s_av --> g_av
     g_av --> ovw
     style prj fill:#E1BEE7,stroke:#424242
     style find fill:#C8E6C9,stroke:#000000
     style check stroke:#000000,fill:#E1BEE7
     style reprj stroke:#000000,fill:#E1BEE7
     style s_av stroke:#000000,fill:#E1BEE7
     style g_av stroke:#000000,fill:#E1BEE7
     style ovw fill:#BBDEFB,stroke:#616161,color:#000000
     style Projecting fill:#EEEEEE, stroke:#424242
     style Averaging fill:#EEEEEE, stroke:#424242
     style subGraph2 fill:#EEEEEE, stroke:#424242
     style subGraph3 fill:#AAAAAA, stroke:#424242
    

Finding acquisitions:

To find the dataset, the script will parse the FOLDERNAME_metadata.yaml file in the data directory. See Getting started for more information.

Project tiles:

TODO: Add description

Averaging:

TODO: Add description

ROI overview:

TODO: Add description