Collection of new use-cases and bug-fixes

[haesleinhuepf]

This PR contains:

• a new test-case for the benchmark
  • I hereby confirm that NO LLM-based technology (such as github copilot) was used while writing this benchmark
• new dependencies in requirements.txt
  • The environment.yml file was updated using the command conda env export > environment.yml
• new generator-functions allowing to sample from other LLMs
• new samples (sample_....jsonl files)
• new benchmarking results (..._results.jsonl files)
• documentation update
• bug fixes

Related github issue (if relevant): closes #0

Short description:

• This is a collection of a couple of pull-requests. I kept them in a separate branch until we rerun the entire benchmark.

How do you think will this influence the benchmark results?

• New test-cases will definitely change the results.

Why do you think it makes sense to merge this PR?

• With this PR, the project is becoming an actual community project.

Before merging this, we need to addd the contributors to the author list:

• Mara Lampert (ScaDS.AI Leipzig / Dresden) @marabuuu contributed
  • Linear intensity profile #82
  • Add test case for translating an image #101
  • Add test case interpolating stack #125
• Seth Hinz (CZ Biohub SF) @shinzlet contributed
  • Add 3 new test cases (identify_centroids, find_closest_neighbors, load_bgr_tif_and_output_rgb) #85
• Ian Francisco Coccimiglio (School of Biomedical Engineering, Faculty of Applied Science, University of British Columbia, Vancouver BC, Canada) @ian-coccimiglio contributed
  • Created model inspection notebook + fix code retrieval from samples #81
  • Extraction of 'Python' from LLM code blocks #92
  • Fixed sum_intensity_projection docstring #117
  • Adjust mean_std_column to accept both pandas and numpy stdev #126
  • [Fixing Test Cases] Allow 0 in label image test cases #134
  • [Fixing-Test-Cases] Image Dimensions reading #127
• llan Theodoro (Chan-Zuckerberg Biohub and the State University of Campinas, Brazil) @ilan-theodoro contributed
  • Add local_maxima_from_distance_transform, flow_field_deformation, and detect_ellipse test cases #86
• Teun A.P.M. Huijben (CZ Biohub San Francisco) @TeunHuijben contributed
  • Added two new test cases: fit_gaussian_to_spot and distance_between_maxima #91
• Jordão Bragantini (Chan Zuckerberg Biohub) @JoOkuma contributed
  • Add new test to register 3D timelapses #90
  • Adding test case for selecting cells that co-express some gene (image intensity) #88
  • Fix typo #87
• Loic A. Royer (CZ Biohub San Francisco) @royerloic added:
  • Added FFT spectrum testcase. It is a hard one :-) #94
• Pradeep Rajasekhar (Centre for Dynamic Imaging, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia, Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3052, Australia) @pr4deepr added:
  • new test cases: image histogram #105
  • mistral_and_deepseek_v2_lite #100
  • Test cases using shapely #132
  • save_image_voxel_size notebook #110
  • Categorise test cases #129
• @rmassei
  • New Test-Case - Metadata Reading plus some basics image processing #142

Big thanks everyone!