Reproducible, high-dimensional imaging in archival human tissue by Multiplexed Ion Beam Imaging by Time-of-Flight (MIBI-TOF)
- 1. Department of Pathology, Stanford University
- 2. Office of the Director, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892
- 3. Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
- 4. Ionpath Inc.
1. SingleChannelMIBI.zip: Single-channel MIBI-TOF images
All folders are labeled as Slide[Number]Stain[Number]_Point[Number]_[TMACoreIndex], where the slide number and stain number correspond to the slide and day of staining, the point number corresponds to the order in which the images were collected for each slide, and the TMA core index corresponds to the ID of the tissue microarray core. Each folder contains single-channel TIFFs for each marker. See paper for details.
2. SegmentationOutput.zip: Segmentation output of MIBI-TOF images
Cell segmentation was performed using Mesmer (Greenwald NF, Nature Biotechnology 2021, https://www.deepcell.org/predict). Output of Mesmer that delineates the single cells in each of the images is included here. Naming convention is the same as above.
3. DataTables.zip: Data tables that are needed to run mpi_ppp_ihc_regression.ipynb
Contains MIBI-TOF data (ionpath_processed_data.csv), MIBI-TOF calibration data (calibration_data.csv), IHC data (ihc_data.csv), and a map of each sample to its tissue type (tissue_data.csv). Also includes cell table output from Mesmer with the cell clusters appended to the table (cell_table_size_normalized_clusters.csv).