Published February 9, 2025
| Version v1
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A multi-modal whole-slide image processing pipeline for quantitative mapping of tissue architecture, histopathology, and tissue microenvironment
Authors/Creators
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1.
University of Pittsburgh
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2.
University of Illinois Urbana-Champaign
Description
This data set is the example data that accompanies the manuscript entitled, "A multi-modal whole-slide image processing pipeline for quantitative mapping of tissue architecture, histopathology, and tissue microenvironment".
1. Data scope
This data set is the example data for multi-modal whole-slide image processing pipeline.
This data is collected for multi-layer reconstruction, multi-tile stitching, multi-cycle alignment and multi-modal registration.
2. Data structure
Folder 'GR1000426_Cy2' contains the 1st cycle of fluorescence and brightfield images.
Folder 'GR1000426_Cy4' contains the 2st cycle of fluorescence and brightfield images.
Folder 'Multi_Cycle_Register' contains the reconstructed and registered images.
Data 'gr1000426.svs' is the corresponding H&E image.
3. Format of the data name
The fluorescence image 'SW480_Cy1_Ro1_Co1_La2_Ex589_Em615.tiff' has a corresponding bright-field image for phase retrieval named ‘SW480_Cy1_Ro1_Co1_La2_Ex000_Em615.tiff’.
For the fluorescence image:
• 'SW480' is the predefined name, usually describing the experimental target.
• 'Cy1' defines the cycle number, indicating the 1st cycle.
• 'Ro1_Co1' defines the tile information, with Ro1 representing the 1st row and Co1 representing the 1st column.
• 'La2' defines the layer information, with La2 indicating the 2nd layer.
• 'Ex589_Em615' defines the excitation and emission wavelengths, with the excitation wavelength being 589 nm and the emission wavelength being 615 nm.
For the bright-field image:
The only difference between the bright-field image and the corresponding fluorescence image is that the excitation wavelength is set to 'Ex000'.
Files
Correction_maps.zip
Additional details
Funding
- National Institutes of Health
- Imaging nanoscale chromatin folding in early carcinogenesis 5R01CA254112-04
- National Institutes of Health
- Three dimensional nanoscale nuclear architecture mapping based taxonomy of precursor lesions for predicting colorectal cancer risk 5R01CA232593-05
Software
- Repository URL
- https://github.com/YangLiuLab/MM_WSI
- Programming language
- MATLAB