README.md

Analyze and Visualize Electrical Brain Stimuluation Data

This repository is designed to work with light-sheet images. Specifaclly GFP-labled-cells as a result of DBS prefromed on Cal-light mice, and tdTomato-labled-cells used as a control. Note you may/likely need to retrain the cellfinder cell_classification network before procceding to Step 5. Please check out my napari repository for how to accomplish network retraining.

All the output data from this repository will be saved in a folder titled mouse_id_Completed_Analysis. This folder will be added to the cellfinder output folder that cellfinder created when you ran it (this should be the file path you use for cellfinder_output_path variable in updateME.py).

Before you can run these files

Create This Anaconda environment

2. brainrender env

conda create -n brainrender python=3.9

pip install brainrender

pip install "numpy<1.24"

Step 1

Clone this repository

Step 2

activate brainrender env

type the following

(brainrender) python path/to/GUI.py

you can drag and drop GUI.py behind the word python

click enter

Step 3

on the imports tab of the GUI

browse your computer and select the cellfinder output director

Step 4

Add a mouse ID

Step 5

Update any features you want in the GUI

Step 6

Click Create 3D Render

OLD STEPS

Create cellfinder Anaconda ENV

1. cellfinder env

conda create -n cellfinder python=3.9

pip install cellfinder

Step 2

updating the information that cellfinder will use to analyze your light-sheet images

follow the instructions for updating the variables here https://docs.brainglobe.info/cellfinder/user-guide/command-line

use this link to understand voxel & orentation variables https://docs.brainglobe.info/cellfinder/image-orientation

open run_cellfinder.bat

update the variables 6 variables, and add extra signal channels if needed

line 6: cellfinder -s, -b, -o, --orentation, -v, --atlas allen_mouse_50um

Step 3

Running cellfinder

open a Anaconda prompt

activate your cellfinder env

for the Denman Lab Neuropixel Aquisition Computer use "conda activate cellfinder2"

drop in run_cellfinder.bat

(cellfinder2) >> path/to/run_cellfinder.bat

click enter

this step may take 2-8 hours to complete per brain

Step 4

Verify correct cell labling using napari

please reference my napari repository for these steps

Step 5

Updating UpdateME.py

Update all the varibales in this folder

Step 6

activate your brainrender env

>> python /path/to/create_3d_brain_render.py