Callaway lab in vitro rabies tracing quantification pipeline. Takes CSV files corresponding to XY point annotations for multichannel imaging experiments.
Step 1: Colocalization test across channels. Groups XY coordinates within user-provided radius (default: 4 pixels) and assigns each XY coordinate features based on which channel these coordinates originate in.
Step 2: Colocalization test across starter cells. Each starter cell is queried against every other starter cell on the dish. If the starter cell falls within a regional radius, it is added to the cluster.
Step 3: Grouping of non-starter cells by region. Each starter cell is assigned a Closest Region ID based on the nearest adjacent starter cell. Each starter cell is given
These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.
What things you need to install the software and how to install them
Python 3
Conda or PIP
numpy
pandas
networkx
scikit-learn
conda install numpy pandas scikit-learn networkx
optional arguments:
-h, --help show this help message and exit
--path path to folder containing CSV
--alignment_radius max xy distance in pixels for two points to be 'aligned' to same cell
--presynaptic_radius Max XY distance which a presynaptic cell be from a starter cell and
still be classified in that starter cell's region
--region_radius Max XY distance in which two starter cells are grouped together into
the same region
- Michael Lingelbach - Initial work - mjlbach
This project is licensed under the MIT License - see the LICENSE.md file for details