This codebase is design to take image- or vector-based ''masks'' and convert them into mask files that can be imported into 2-photon imaging software (PrairieView by Bruker) and direct the microscope system to selectively "expose" regions of a sample to laser power according to the mask.
The easiest way to start will be to download this code, and use Anaconda to setup a python environment. Then use a jupyter notebook to load and run the conversion code. You can do this via the following steps:
-
Download a release or clone this repository into a folder (e.g.
.../cmp/) on your computer.- Download the latest release here.
- Note: If you clone this repository, you will need to import the submodules
via the following commands:
git submodule init git submodule update
-
Download and install Anaconda (individual edition) if you do not already have it
-
From the anaconda prompt
cdto this repository directory, then run one the following commands.conda env create --prefix ./env --file env.yml
If issues occur with the first method here you can try generating the enviornment from the explicit package list:
conda env create --prefix ./env --file .env-explicit.txt
-
Activate the anaconda enviornment by the following command
conda activate ./env
-
Open a jupyter notebook by entering the following command
jupyter lab getting_started.ipynb
-
Once in the jupyter notebook run and edit the cells to see how to use the mask generation codebase.
- Add more examples of using parameters.
- Add documentation to classes and functions.
- Handling additional edge cases.
- Create example jupyter notebook.