View Labeled IHC images of RCC (public)

2012-03-09 11:27 by jetic | Version 4 | Rating Empty StarEmpty StarEmpty StarEmpty StarEmpty StarEmpty Star
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Summary

Labeled immunohistochemically stained tissue micro array images for nucleus detection and classification

DOI (more info at datacite)
10.5881/LABELED-IHC-IMAGES-OF-RCC
License
CC0
Dependencies
Tags
Carcinoma Cell Classification Clear compuational detection immunohistochemistry pathology Renal
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Original Data Format
zip
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Names
Data (first 10 data points)
    ZIP archive immunohistochemical_images/, immunohistochemical_images/Mib-1 on Human Renal Clear Cell Carcinoma/, immunohistochemical_images/Mib-1 on Human Renal Clear Cell Carcinoma/Pathologist1/, immunohistochemical_images/Mib-1 on Human Renal Clear Cell Carcinoma/Pathologist1/spots_A_08_1_top_left.xml, immunohistochemical_images/Mib-1 on Human Renal Clear Cell Carcinoma/Pathologist1/spots_B_05_5_top_left.xml, immunohistochemical_images/Mib-1 on Human Renal Clear Cell Carcinoma/Pathologist1/spots_B_10_3_top_left.xml, immunohistochemical_images/Mib-1 on Human Renal Clear Cell Carcinoma/Pathologist1/spots_B_11_2_top_left.xml, immunohistochemical_images/Mib-1 on Human Renal Clear Cell Carcinoma/Pathologist1/spots_B_12_6_top_left.xml, immunohistochemical_images/Mib-1 on Human Renal Clear Cell Carcinoma/Pathologist1/spots_C_07_6_top_left.xml, immunohistochemical_images/Mib-1 on Human Renal Clear Cell Carcinoma/Pathologist1/spots_C_10_8_top_left.xml, immunohistochemical_images/Mib-1 on Human Renal Clear Cell Carcinoma/Pathologist1/spots_C_11_6_top_left.xml, immunohistochemical_images/Mib-1 on Human Renal Clear Cell Carcinoma/Pathologist2/, immunohistochemical_images/Mib-1 on Human Renal Clear Cell Carcinoma/Pathologist2/spots_A_08_1_top_left.xml, immunohistochemical_images/Mib-1 on Human Renal Clear Cell Carcinoma/Pathologist2/spots_B_05_5_top_left.xml, immunohistochemical_images/Mib-1 on Human Renal Clear Cell Carcinoma/Pathologist2/spots_B_10_3_top_left.xml, immunohistochemical_images/Mib-1 on Human Renal Clear Cell Carcinoma/Pathologist2/spots_B_11_2_top_left.xml, immunohistochemical_images/Mib-1 on Human Renal Clear Cell Carcinoma/Pathologist2/spots_B_12_6_top_left.xml, immunohistochemical_images/Mib-1 on Human Renal Clear Cell Carcinoma/Pathologist2/spots_C_07_6_top_left.xml, immunohistochemical_images/Mib-1 on Human Renal Clear Cell Carcinoma/Pathologist2/spots_C_10_8_top_left.xml, immunohistochemical_images/Mib-1 on Human Renal Clear Cell Carcinoma/Pathologist2/spots_C_11_6_top_left.xml, immunohistochemical_images/Mib-1 on Human Renal Clear Cell Carcinoma/spots_A_08_1_top_left.png, immunohistochemical_images/Mib-1 on Human Renal Clear Cell Carcinoma/spots_B_05_5_top_left.png, immunohistochemical_images/Mib-1 on Human Renal Clear Cell Carcinoma/spots_B_10_3_top_left.png, immunohistochemical_images/Mib-1 on Human Renal Clear Cell Carcinoma/spots_B_11_2_top_left.png, immunohistochemical_images/Mib-1 on Human Renal Clear Cell Carcinoma/spots_B_12_6_top_left.png, immunohistochemical_images/Mib-1 on Human Renal Clear Cell Carcinoma/spots_C_07_6_top_left.png, immunohistochemical_images/Mib-1 on Human Renal Clear Cell Carcinoma/spots_C_10_8_top_left.png, immunohistochemical_images/Mib-1 on Human Renal Clear Cell Carcinoma/spots_C_11_6_top_left.png, immunohistochemical_images/Readme.txt
Description

The images show immunohistochemical stainings (e.g. MIB-1 staining) on several tissue micro array (TMA) spots.

Blue dots on the images are cell nuclei, negative for the protein, brown ones are positive nuclei.

Additionally, some nuclei belong to malignant cancerous cells and some belong to benign cells (the class of a nucleus). The location and class of all nuclei in the images is written in the .XML files. Each nucleus has a location and label (0 for benign, 1 for malignant).

Note that besides a big overlap between different pathologists, there are some disagreements in the location and class of a nucleus.

The task is to improve state-of-the-art computer vision and image processing to be capable of automatically detect and classify cell nuclei in such type of images.

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Publications
    Data Source
    University Hospital Zurich, Switzerland.
    Measurement Details

    The tissue microarray block was generated in a trial from the University Hospital Zurich. The TMA slides were immunohistochemically stained with the MIB-1 (Ki-67) antigen. Scanning was performed on a Nanozoomer C9600 virtual slide light microscope scanner from HAMAMATSU. The magnification of 40x resulted in a per pixel resolution of 0.23μm. The tissue microarry was tiled into 133 single spots of size 3000 × 3000 pixel, representing one patient each. 8 spots were randomely selected and quartered for manual labeling, training and testing.

    Usage Scenario
    revision 1
    by jetic on 2012-03-08 12:06
    revision 2
    by jetic on 2012-03-08 12:12
    revision 3
    by jetic on 2012-03-08 12:15
    revision 4
    by jetic on 2012-03-09 11:27

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    Acknowledgements

    This project is supported by PASCAL (Pattern Analysis, Statistical Modelling and Computational Learning)
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