Add notebook for nuclei segmentation using Voronoi-Otsu-Labeling, file loading, and result saving.

[github-actions]

^{This message was generated by git-bob (version: 0.9.0, model: gpt-4o-2024-08-06, log), an experimental AI-based assistant. It can make mistakes and has limitations. Check its messages carefully.}

The changes include the addition of a Jupyter notebook file, nuclei_segmentation_analysis.ipynb, which performs nuclei segmentation on a loaded image file using the Voronoi-Otsu-Labeling method. The image file, saved as human_mitosis_small.png, is processed by extracting the first channel, applying segmentation, and saving the resulting labels as an RGB PNG named labeled_nuclei.png. However, an error related to an undefined np was encountered during the conversion of the labeled image to RGB, which needs attention. The notebook provides necessary steps and outputs for nuclei segmentation analysis, aligning with the requirements of issue #13.

closes #13

[haesleinhuepf]

Ok, this is almost perfect. Please visualize the input image using stackview.insight and also visualize the resulting labeled_image. Last but not least, you forgot to import nump as np at the beginning of the notebook.

git-bob implement this

[github-actions]

^{This message was generated by git-bob (version: 0.9.0, model: gpt-4o-2024-08-06, log), an experimental AI-based assistant. It can make mistakes and has limitations. Check its messages carefully.}

In this set of changes, I added the missing import for numpy in the nuclei_segmentation_analysis.ipynb notebook and visualized the input and labeled images with stackview.insight, while also correcting the metadata for execution. Additionally, two new image files were created: and . Also, a link to the nuclei_segmentation_analysis.ipynb file was added.

During solving this task, the following errors occurred:

• Error during {'action': 'download', 'source_url': 'https://github.com/haesleinhuepf/git-bob-playground/blob/git-bob-mod-pWGnb0jNr4/nuclei_segmentation_analysis.ipynb', 'target_filename': 'nuclei_segmentation_analysis.ipynb'}: 422 {"message": "Invalid request.\n\n\"sha\" wasn't supplied.", "documentation_url": "https://docs.github.com/rest/repos/contents#create-or-update-file-contents", "status": "422"}

      Traceback (most recent call last):
      File "/home/runner/work/git-bob-playground/git-bob-playground/git-bob/src/git_bob/_github_utilities.py", line 837, in download_to_repository
        contents = repo.get_contents(target_filename)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/github/Repository.py", line 2204, in get_contents
        headers, data = self._requester.requestJsonAndCheck(
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/github/Requester.py", line 550, in requestJsonAndCheck
        return self.__check(*self.requestJson(verb, url, parameters, headers, input, self.__customConnection(url)))
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/github/Requester.py", line 611, in __check
        raise self.createException(status, responseHeaders, data)
    github.GithubException.UnknownObjectException: 404 {"message": "Not Found", "documentation_url": "https://docs.github.com/rest/repos/contents#get-repository-content", "status": "404"}
  During handling of the above exception, another exception occurred:
  Traceback (most recent call last):
  
  File "/home/runner/work/git-bob-playground/git-bob-playground/git-bob/src/git_bob/_ai_github_utilities.py", line 480, in solve_github_issue
  
  download_to_repository(repository, branch_name, source_url, target_filename)
  
  File "/home/runner/work/git-bob-playground/git-bob-playground/git-bob/src/git_bob/_github_utilities.py", line 843, in download_to_repository
  
  repo.create_file(target_filename, commit_message, image_content, branch=branch_name)
  
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/github/Repository.py", line 2457, in create_file
  
  headers, data = self._requester.requestJsonAndCheck(
  
  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/github/Requester.py", line 550, in requestJsonAndCheck
  
  return self.__check(*self.requestJson(verb, url, parameters, headers, input, self.__customConnection(url)))
  
  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/github/Requester.py", line 611, in __check
  
  raise self.createException(status, responseHeaders, data)
  
  github.GithubException.GithubException: 422 {"message": "Invalid request.\n\n"sha" wasn't supplied.", "documentation_url": "https://docs.github.com/rest/repos/contents#create-or-update-file-contents", "status": "422"}
  
  

• Error during {'action': 'download', 'source_url': 'https://github.com/haesleinhuepf/git-bob-playground/blob/git-bob-mod-pWGnb0jNr4/human_mitosis_small.png?raw=true', 'target_filename': 'human_mitosis_small.png'}: 422 {"message": "Invalid request.\n\n\"sha\" wasn't supplied.", "documentation_url": "https://docs.github.com/rest/repos/contents#create-or-update-file-contents", "status": "422"}

      Traceback (most recent call last):
      File "/home/runner/work/git-bob-playground/git-bob-playground/git-bob/src/git_bob/_github_utilities.py", line 837, in download_to_repository
        contents = repo.get_contents(target_filename)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/github/Repository.py", line 2204, in get_contents
        headers, data = self._requester.requestJsonAndCheck(
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/github/Requester.py", line 550, in requestJsonAndCheck
        return self.__check(*self.requestJson(verb, url, parameters, headers, input, self.__customConnection(url)))
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/github/Requester.py", line 611, in __check
        raise self.createException(status, responseHeaders, data)
    github.GithubException.UnknownObjectException: 404 {"message": "Not Found", "documentation_url": "https://docs.github.com/rest/repos/contents#get-repository-content", "status": "404"}
  During handling of the above exception, another exception occurred:
  Traceback (most recent call last):
  
  File "/home/runner/work/git-bob-playground/git-bob-playground/git-bob/src/git_bob/_ai_github_utilities.py", line 480, in solve_github_issue
  
  download_to_repository(repository, branch_name, source_url, target_filename)
  
  File "/home/runner/work/git-bob-playground/git-bob-playground/git-bob/src/git_bob/_github_utilities.py", line 843, in download_to_repository
  
  repo.create_file(target_filename, commit_message, image_content, branch=branch_name)
  
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/github/Repository.py", line 2457, in create_file
  
  headers, data = self._requester.requestJsonAndCheck(
  
  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/github/Requester.py", line 550, in requestJsonAndCheck
  
  return self.__check(*self.requestJson(verb, url, parameters, headers, input, self.__customConnection(url)))
  
  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/github/Requester.py", line 611, in __check
  
  raise self.createException(status, responseHeaders, data)
  
  github.GithubException.GithubException: 422 {"message": "Invalid request.\n\n"sha" wasn't supplied.", "documentation_url": "https://docs.github.com/rest/repos/contents#create-or-update-file-contents", "status": "422"}