This code is used to preprocess tiff files generated by a two-photon microscope. It can (1) download tiffs from an Azure storage location using data in a experimental metafile, (2) process tiffs using imageJ to find the maximum Z-projection and save into chunks for further processing, and (3) use suite2p to perform registration and cell detection.
Raw and processed files are saved with a file structure as recommended by xxx.
Navigate into the src directory and run the program from the command line.
It is recommended to run the script on a machine with at least 64GB RAM and a GPU.
This project makes ample use of imageJ and suite2p.
This README file was generated with https://readme.so/editor
Contributions are always welcome!
Please email me if you are interested.
Please adhere to this project's code of conduct.