BRISC - Barcoded Rabies in Situ Connectomics

Installation

This should work with any python > 3.8 and was tested with python version up to 3.11. To install clone the repository and install it with pip:

git clone git@github.com:znamlab/brisc.git
cd brisc
pip install .

If you want to modify the code, there are a dev install option to install the requirements for pre-commit:

pip install -e ".[dev]"
pre-commit install

Get the data

Download the data from figshare. Unzip and open the brisc/config.yml file to change the file path to the folder where you extracted the data.

Download external data

For Fig S1, data from the previously published viral libraries must be downloaded and preprocessed by running brisc/barcode_library_processing/convert_external_libraries.ipynb.

Generate the figures

The manuscript_figures folder contains the notebooks to regenerate all data figures. In each notebook the DATA_ROOT will have to be updated to the path to the folder where the data is located.

System requirements:

Tested on:

Operating System: Rocky Linux 8.7 (Green Obsidian)

Architecture: x86-64

A full software dependency list with version numbers is available in package_list.txt

Expected installation time: ~10 minutes

Required non-standard hardware:

Figure 2 requires a minimum of 64GB RAM to reproduce overview images

Expected run time per figure:

Fig. 1. ~ 2 minutes

Fig. 2. ~ 10 minutes

Fig. 3. ~ 10 minutes

Fig. 4. ~ 20 minutes

Fig. 5. ~ 20 minutes

Fig. 6. ~ 20 minutes

Supp Fig. 1. ~ 2 minutes

Supp Fig. 3. ~ 10 minutes

Supp Fig. 4. ~ 10 minutes

Supp Fig. 6. ~ 10 minutes