donato lab [ca] imaging tools
Project description
manifolds project @ Donato lab
Installation
Recommended steps
-
Open a command-line interface preferably inside the conda enviroment on your operating system (Windows, Mac)
-
Use command-line to make a conda enviorment for running manifolds project:
conda create -n manifolds python=3.8
- Activate environment:
conda activate manifolds
- Install dependencies (might have to do them 1 at a time; eventually will have a script for this)
pip install: matplotlib, os, numpy, scipy, tqdm, sklearn, pickle, parmap, networkx, pandas, cv2
- Install jupyter notebook
conda install -c anaconda jupyter
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Download and unzip the Donatolab binarization repo (https://github.com/donatolab/manifolds, click onthe green "Code" button)
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Start jupyer notebook by typing it in at the command line
jupyter notebook
- Navigate to the folder where the code unzipped and click on this file to start the jupyter notebook:
"Binarize_Suite2p_Inscopix.ipynb"
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Run the first cell and then input the location of your suite2p folder in 2nd cell. Run the rest of the notebook.
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The code will save 2 files: binarized_traces.npz (a python numpy file) and binarized_traces.mat (a matlab file).
10(Optional) You can then use the last cell to visualize the traces and binarized versions for any specific cell.
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