MMV_Im2Im: An Open Source Microscopy Machine Vision Toolbox for Image-to-Image Transformation

This dataset contains trained deep learning models and sample data for the manuscript "MMV_Im2Im: An Open Source Microscopy Machine Vision Toolbox for Image-to-Image Transformation". Please find the software and more information including tutorials here: https://github.com/MMV-Lab/mmv_im2im.

sample_data.zip includes the following datasets:

• Labelfree prediction of nuclear structure from 2D/3D brighteld images
  • 2D
    • https://zenodo.org/record/6139958#.Y78QJKrMLtU
    • https://zenodo.org/record/6140064#.Y78YeqrMLtU
    • Both repositories have a Creative Commons Attribution 4.0 International License
  • 3D
    • https://open.quiltdata.com/b/allencell/packages/aics/hipsc_single_cell_image_dataset
    • Terms of use: https://www.allencell.org/terms-of-use.html
    • "Your use of the Content, including creation of derivative works of the services, data and tools, must be for research or other noncommercial purposes unless it is otherwise set forth in these Terms or agreed to in writing by the Allen Institute."
• 2D semantic segmentation of tissues from H&E images
  • https://www.kaggle.com/datasets/sani84/glasmiccai2015-gland-segmentation
  • "The dataset used in this competition is provided for research purposes only. Commercial uses are not allowed.
    If you intend to publish research work that uses this dataset, you must cite our review paper to be published after the competition"
• Instance segmentation
  • 2D
    • https://bbbc.broadinstitute.org/BBBC010
    • Terms of use: https://bbbc.broadinstitute.org/
    • "Researchers are encouraged to use these image sets as reference points when developing, testing, and publishing new image analysis algorithms for the life sciences."
  • 3D
    • https://open.quiltdata.com/b/allencell/packages/aics/hipsc_single_cell_image_dataset
    • Terms of use: https://www.allencell.org/terms-of-use.html
    • "Your use of the Content, including creation of derivative works of the services, data and tools, must be for research or other noncommercial purposes unless it is otherwise set forth in these Terms or agreed to in writing by the Allen Institute."
• Compare semantic segmentation and instance segmentation
  • https://open.quiltdata.com/b/allencell/packages/aics/hipsc_single_cell_image_dataset
  • Terms of use: https://www.allencell.org/terms-of-use.html
  • "Your use of the Content, including creation of derivative works of the services, data and tools, must be for research or other noncommercial purposes unless it is otherwise set forth in these Terms or agreed to in writing by the Allen Institute."
• Unsupervised semantic segmentation
  • https://open.quiltdata.com/b/allencell/packages/aics/hipsc_single_cell_image_dataset
  • Terms of use: https://www.allencell.org/terms-of-use.html
  • "Your use of the Content, including creation of derivative works of the services, data and tools, must be for research or other noncommercial purposes unless it is otherwise set forth in these Terms or agreed to in writing by the Allen Institute."
• Generating synthetic images
  • https://open.quiltdata.com/b/allencell/packages/aics/hipsc_single_cell_image_dataset
  • Terms of use: https://www.allencell.org/terms-of-use.html
  • "Your use of the Content, including creation of derivative works of the services, data and tools, must be for research or other noncommercial purposes unless it is otherwise set forth in these Terms or agreed to in writing by the Allen Institute."
• Image denoising
  • https://csbdeep.bioimagecomputing.com/scenarios/
  • Two datasets: "Denoising in 3D (Planaria nuclei)" and "Denoising in 3D (Tribolium nuclei)"
  • Terms of use: http://csbdeep.bioimagecomputing.com/
  • "The entire CSBDeep toolbox is fully open source and intended to be used from either Python or Fiji."
• Imaging modality transformation
  • https://zenodo.org/record/4624364#.Y9bWOoHMIqJ
  • Two datasets: "Confocal_2_STED.zip" (Microtubule and Nuclear_Pore_complex)
  • Repository has a Creative Commons Attribution 4.0 International License
• Staining transformation:
  • https://zenodo.org/record/4751737#.Y9gbv4HMLVZ
  • Dataset "BC-DeepLIIF_Training_Set.zip" and "BC-DeepLIIF_Validation_Set.zip"
  • Repository has a Creative Commons Attribution 4.0 International License