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ActiveBrainAtlas2 / activebrainatlasadmin

This is the ActiveBrainAtlas database portal. This project provides the admin area to edit data associated with the Active Brain Atlas project. It also provides the REST API.
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Installing and running cell_extractor #140

Open yoavfreund opened 1 year ago

yoavfreund commented 1 year ago

Cell_extractor is in it's own github repository, this is a good idea, as it will allow users outside DKLab to install and run it without needing to install the pipeline/database etc.

We are in the process of cleaning out the code and creating documentation.

The first step is to make sure that the repository can be installed and run.

This means anybody with acccess to the repository can:

  1. git clone the repository
  2. Read a README.md file that contains directions for what needs to be installed. Including requirements.txt, external packages, virtual environments, other DKLab packages, setting environmental variables etc. Everything that is needed in order to install and run cell_extractor on a NEW machine.
  3. Some small test files to be used for testing. (small because they will be stored on github)
  4. Documentation for how to run the main scripts.

Right now, I can't make anything work. I figured I need cv2, that got rid of some import errors, but I still get errors even when I run scripts with the -h flag:

(cv) MacBook-Pro-9:scripts yoavfreund$ python generate_tif_tiles.py -h Traceback (most recent call last): File "generate_tif_tiles.py", line 4, in from lib.TiffSegmentor import TiffSegmentor ModuleNotFoundError: No module named 'lib' (cv) MacBook-Pro-9:scripts yoavfreund$ python create_example_for_one_section.py -h Traceback (most recent call last): File "create_example_for_one_section.py", line 4, in from cell_extractor.ExampleFinder import create_examples_for_one_section ModuleNotFoundError: No module named 'cell_extractor' (cv) MacBook-Pro-9:scripts yoavfreund$

Yoav

drinehart1 commented 1 year ago

Reassigned to Kui (needs to be done by 28-NOV-2022)

drinehart1 commented 1 year ago

Kui has finished README; needs testing [by Yoav & David] after 5-DEC-2022