This page os meant to show the real structure of the pipeline, so that running the pipeline is easier to understand.

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The overall structure of the data created by HeureCa:

<root_directory>/
├── <experiment_name>_1.tif
├── <experiment_name>_2.tif
├── <experiment_name>.mesc
└── merged_tiffs/
    ├── merged_<group_1>/
    │   └── merged_<group_1>.tif
    ├── merged_<group_2>/
    │   └── merged_<group_2>.tif
    └── ...

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Concrete directory structure:

Here's a simplified layout of the folder structure for Hyperstim's data:

Hyperstim
└── data_analysis/
        └── <experiment_name>/
            ├── merged_tiffs/
            │   ├── merged_<experiment_name>/
            │   │   └── merged_<experiment_name><concatenated tiff numbers>.tif
            │   │           └── suite2p/
            │   │               └── plane0/
            │   │                   ├── data.bin
            │   │                   ├── F.npy
            │   │                   ├── ops.npy
            │   │                   ├── stat.npy
            │   │                   ├── iscell.npy
            │   │                   ├── spks.npy
            │   │                   ├── iscell.npyFneu
            │   │                   ├── Fall.npy
            │   │                   └── F0.npy
            │   └── cellreg_files/
            │       └── cellreg_files/
            │               ├── cellreg_input_<experiment_name>_<tif number>.mat
            │               └── Figures/
            ├── trigger.txt
            ├── stim.txt
            ├── frameNo.txt
            ├── fileID.txt
            └── <experiment_name>.mesc

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In summary:

• root_directory is the main directory where all your experiment data is stored
• Each experiment has its own folder, which contains the original TIFF files, the .mesc file, and a merged_tiffs folder.
• The merged_tiffs folder contains subfolders for each group of merged TIFF files, where each subfolder has a merged TIFF file named according to the group. Each merged TIFF file has its own Suite2p output directory containing the necessary files for analysis.
• The cellreg files are stored in a separate cellreg_files folder, which contains the input files for CellReg and the generated figures separately in the Figures folder.