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Mesoscopy is an open-source package for the analysis of mesoscale calcium recordings. It handles the preprocessing of mesoscale recording files to extract ∆F responses, the anatomical registration of recordings to the Allen Brain atlas as well as analysis of recordings captured at rest or with behaviour.

Prerequisites

Mesoscopy works best with data acquired in the NWB format. Alternatively, recordings acquired as HDF5 files compatible with mesoscopy's raw data schema may be used.

Dual-channel recordings with an accompanying haemodynamic response channel (e.g. using both 470nm and 405nm excitation for GCaMP) will be automatically separated during preprocessing and yield a corrected ∆F signal.

An example acquisition script (designed for FLIR Grasshopper cameras) can be found here.

Installing mesoscopy

The recommended way to install mesoscopy is by using pipx (https://pypa.github.io/pipx/). pipx will create an isolated python environment from which mesoscopy will run, leaving the system python alone. This is the recommended way to install mesoscopy, as it will not interfere with any other python packages you may have installed on your system.

On Linux

1. Install pipx.

   • On Ubuntu / Debian:

     sudo apt update
     sudo apt install pipx
     pipx ensurepath
     sudo pipx ensurepath

   • On Fedora:

     sudo dnf install pipx
     pipx ensurepath
     sudo pipx ensurepath

   • For other distributions, install pipx with pip:

     python3 -m pip install --user pipx
     python3 -m pipx ensurepath
     sudo pipx ensurepath

2. Install mesoscopy.

   pipx install mesoscopy

On MacOS

1. Install pipx with homebrew.

   brew install pipx
   pipx ensurepath
   sudo pipx ensurepath

2. Install mesoscopy.

   pipx install mesoscopy

On Windows

With Windows, you have two choices. You can either use mesoscopy with the Windows Subsystem for Linux (WSL) and follow the instructions above for installing mesoscopy on Linux (recommended), or you can run mesoscopy directly on Windows via PowerShell. The choice is of course yours, but you should bear in mind that mesoscopy primarily targets Unix-like OSs (Linux & MacOS) at the moment, so while everything should work fine on Windows, your mileage may vary.

To install mesoscopy directly on Windows, first install pipx using Scoop:

scoop install pipx
pipx ensurepath

Then install mesoscopy via pipx:

pipx install mesoscopy

Usage

For detailed documentation on how to use mesoscopy, please refer to our documentation.

To see all available mesoscopy commands, run

mesoscopy --help

mesoscopy commands are self-documenting. Run mesoscopy <command> --help to get more information or see available sub-commands.

Upgrading

Use pipx to upgrade mesoscopy:

pipx upgrade mesoscopy

Contributing

Mesoscopy is currently closed to PRs, except bugfixes. Please open an issue if you wish to contribute.

Funders