snlc / ivrt_image_pipeline

In vitro rabies tracing quantification pipeline

In Vitro Rabies Tracing Quantification Pipeline

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

Getting Started

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.

Prerequisites

What things you need to install the software and how to install them

Python 3
Conda or PIP
numpy
pandas
networkx
scikit-learn

Installing

conda install numpy pandas scikit-learn networkx

Command line arguments

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

Authors

• Michael Lingelbach - Initial work - mjlbach

License

This project is licensed under the MIT License - see the LICENSE.md file for details