Typical workflow

A typical workflow involves the following steps:

1. Conversion from RAW to HDF5
2. Motion correction
3. ROI drawing
4. Signal extraction and decontamination
5. ΔF/F₀ computation

This provides a very broad overview of what the software provides. For a step-by-step guide going through each of these commands, you should read the tutorials.

Conversion from RAW to HDF5

This step converts the RAW binary files coming from a 2-photon scope into the HDF5 file format for easier storage.

Command:

drim2p convert raw /path/to/your/recordings.raw

Motion correction

This step corrects for motion artifacts in recordings.

Command:

drim2p motion correct /path/to/your/recordings.h5 --settings-path /path/to/your/settings.toml

ROI drawing

This step allows drawing ROIs around cells for further preprocessing.

Command:

drim2p draw roi /path/to/your/recordings.h5

Signal extraction and decontamination

This step extracts "true" signals for the cells denoted by the drawn ROIs.

Command:

drim2p extract signal /path/to/your/recordings.h5

ΔF/F₀ computation

This step compute ΔF/F₀ for extracted signals.

Command:

drim2p delta /path/to/your/recordings.h