README.md

brainrender

using cellfinder output files to render 3D models of fluorescently labeled cells

Starting from scratch

1. Create anacoonda envrioment

This will create an env where you can render 3D models of you labled cells

open an Anaconda prompt

>> conda create -n brainrender python=3.9

>> conda activate brainrender

>> pip install brainrender

2. Download the batch file from this repository

This batch file will

Changes to make to brainrender.py file before running

1. Change Path to cellfinder_output points.npy file

when you run cellfinder, the data will be saved to an output directory that you specified in the batch file. Inside of this output directory will be a folder titled points, inside that will be a file called (points.npy). on line 21 of brainrender.py, change cells_path to the path of that points.npy file

line 21 cells_path = r"C:\Users\denma\Desktop\Grant\cellfinder\cellfinder_output\points\points.npy"

2. change the path to where your locally stored allen mouse atlas

to find the local location of the allen_mouse_50um atlas on your computer. go to the finder and type in allen_mouse_50um, then copy that path and replace line 25 in brainrender.py with that path

line 25 allen_mouse_50um = r'C:\Users\denma.brainglobe\allen_mouse_50um_v1.2'

Run updated brainrender.py file

>> conda activate brainrender

>> python /path/to/your/brainrender.py