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Getting Started

Mesoscopy is an open-source package for the analysis of mesoscale calcium recordings. It preprocesses mesoscale recording files to extract ∆F responses, registers recordings to the Allen Brain atlas, and analyses recordings captured at rest or with behaviour.

Prerequisites

Mesoscopy works best with data acquired in the NWB format. It also takes recordings acquired as HDF5 files that follow mesoscopy's raw data schema.

Dual-channel recordings with a haemodynamic response channel, such as 470nm and 405nm excitation for GCaMP, are separated during preprocessing and yield a corrected ∆F signal.

An example acquisition script for FLIR Grasshopper cameras is here.

Installing mesoscopy

Install mesoscopy with pipx. pipx creates an isolated python environment for mesoscopy to run from and leaves the system python alone, so it does not interfere with any other python packages 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
     

   • On 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

On Windows, use mesoscopy under the Windows Subsystem for Linux (WSL) and follow the Linux instructions above. mesoscopy targets Unix-like systems first, so this is the path we recommend.

To run mesoscopy directly on Windows instead, install pipx with Scoop in PowerShell.

scoop install pipx
pipx ensurepath

Then install mesoscopy with pipx.

pipx install mesoscopy

Next steps

The typical workflow guide takes you through the processing steps for analysing mesoscale recordings with mesoscopy.

The how-to guides go deeper into individual aspects of analysis, including quality control. If you are about to start acquiring data, or want to convert existing data to a format mesoscopy reads, start with the data schema and converting videos to HDF5 guides.