cellfinder

If your running this from the Denman Lab Neuropixel Aquisition Computer skip Step 1

These are the steps for running the open source cellfinder package on Estim collected lightsheet images

Step 1

Create an Anaconda enviroment

open Anaconda prompt

>> conda create -n cellfinder python=3.9

>> conda activate cellfinder

>> pip install cellfinder

step 2

Edit the batch file in this repository in the following way to match your data

line 4: conda call (your cellfinder env name)

line 6: Update all 6 varaibles (-s, -b, -o, --orentation, -v, --atlas)

-s path/to/signal/channel (directory path to .tif photos of gfp channel)

-s path/to/second-signal/channel (directory path to .tif photos of tdTomato channel)

-b path/to/autoflourecent/channel (directory path to .tif photos of autoflourecent/background channel)

-o path/to/where you want/cellfinder output files to save to/

--orentation Three letters representing orenation of your .tiff images (example: spl)

-v Three numberes representing the voxel spacing of your .tiff images (example: 5 1 1)

Step 2

Open Anaconda prompt

Drag and drop the updated batch file in this repository into the anaconda prompt

This script will take the cellfinder summary.csv file for your GFP and tdTomato signal channales, and create a pandas df that shows you the percent cells labled in GFP compared to the percent of cells labled in tdTomato (control) for all brain regions.

How to use this script

step 1

change the path to your cellfinder output summary.csv path, for poth gfp and tdTomato channels

gfp_df = pd.read_csv("/path/to/your/datas/gfp_summary.csv")

tdTomato_df = pd.read_csv("/path/to/your/datas/tdTomato_summary.csv")

step 2

change the path variable to where you want this csv file to be saved locally

path = '/path/to/where/you/want/output csv/saved to/