HyReCo - Hybrid re-stained and consecutive histological serial sections

Citation Author(s):
Jeroen
van der Laak
Radboud University Medical Center
Johannes
Lotz
Fraunhofer MEVIS
Nick
Weiss
Fraunhofer MEVIS
Stefan
Heldmann
Fraunhofer MEVIS
Submitted by:
Johannes Lotz
Last updated:
Tue, 12/14/2021 - 05:55
DOI:
10.21227/pzj5-bs61
Data Format:
License:
0
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Abstract 

This dataset was acquired at the Radboud University Medical Center, Nijmegen, the Netherlands and enriched with landmarks by Fraunhofer MEVIS. It consists of nine datasets of consecutive sections, each containing four slides stained with H&E, CD8, CD45, Ki67, respectively. In addition, PHH3-stained slides have been produced by removing the cover slip from the H&E-stained slide, bleaching the H&E stain, re-staining the same section with PHH3 and scanning it again, similar to the T-CyCIF technique [@gerdes_highly_2013; @lin_highly_2018] that is well established in fluorescence imaging. For each of these sections , 11--19 landmarks (138 per stain, 690 in total) have been placed manually on corresponding structures and verified by two experienced researchers.

Finding the same points across of several consecutive slides is quite difficult, because care must be taken to locate a similar point in all slides simultaneously. In contrast to these consecutive sections, an image pair of re-stained sections contains the same cells and nuclei such that a one-to-one correspondence can be found for most structures. To overcome the limitations in annotation accuracy imposed by the simultaneous annotation of consecutive and re-stained slides, further re-stained slides were annotated. For this, an additional number of 2303 annotations were produced for 54 additional image pairs of H&E-PHH3 (ca. 43 annotations per pair). 

The requirement for ethical approval was waived by the IRB of Radboudumc, Nijmegen, the Netherlands, under file number 2020-6972.

Instructions: 

# HyReCo - Hybrid Re-stained and Consecutive Data

The **HyReCo** dataset contains whole slide images of consecutive and restained slides. There are nine different cases (29, 108, 361, 464, 533, 611, 628, 644, 679) with 4 consecutive slices each. They were stained with HE, CD8, KI67, CD45. Additionally, the HE slice was restained with PHH3. All versions were scanned and are available as whole slide images in the BigTIFF format.

There are annotations for each image in an additional CSV file. These files contain lists of point annotations that attempt to mark the same location in all images of a single case. Each line describes a point annotation in world coordinates (x,y,z). The unit is mm. The origin of the coordinate system is the upper left corner of the image.

The **HyReCo-Additional** dataset is structured in the same way, but does only contain restained image pairs of HE and PHH3. There are 54 different cases for this additional dataset with point annotations for each image.

## HyReCo file structure

HyReCo/

- CD45/
- 108.csv
- 108.tif
- 29.csv
- 29.tif
- 361.csv
- 361.tif
- 464.csv
- 464.tif
- 533.csv
- 533.tif
- 611.csv
- 611.tif
- 628.csv
- 628.tif
- 644.csv
- 644.tif
- 679.csv
- 679.tif
- CD8/
- 108.csv
- 108.tif
- 29.csv
- 29.tif
- 361.csv
- 361.tif
- 464.csv
- 464.tif
- 533.csv
- 533.tif
- 611.csv
- 611.tif
- 628.csv
- 628.tif
- 644.csv
- 644.tif
- 679.csv
- 679.tif
- HE/
- 108.csv
- 108.tif
- 29.csv
- 29.tif
- 361.csv
- 361.tif
- 464.csv
- 464.tif
- 533.csv
- 533.tif
- 611.csv
- 611.tif
- 628.csv
- 628.tif
- 644.csv
- 644.tif
- 679.csv
- 679.tif
- KI67/
- 108.csv
- 108.tif
- 29.csv
- 29.tif
- 361.csv
- 361.tif
- 464.csv
- 464.tif
- 533.csv
- 533.tif
- 611.csv
- 611.tif
- 628.csv
- 628.tif
- 644.csv
- 644.tif
- 679.csv
- 679.tif
- PHH3/
- 108.csv
- 108.tif
- 29.csv
- 29.tif
- 361.csv
- 361.tif
- 464.csv
- 464.tif
- 533.csv
- 533.tif
- 611.csv
- 611.tif
- 628.csv
- 628.tif
- 644.csv
- 644.tif
- 679.csv
- 679.tif

## HyReCo-Additiona file structure

HyReCo-Additional/

- HE/
- 108.csv
- 108.tif
- 128.csv
- 128.tif
- 147.csv
- 147.tif
- 155.csv
- 155.tif
- 157.csv
- 157.tif
- 158.csv
- 158.tif
- 168.csv
- 168.tif
- 172.csv
- 172.tif
- 208.csv
- 208.tif
- 237.csv
- 237.tif
- 241.csv
- 241.tif
- 244.csv
- 244.tif
- 245.csv
- 245.tif
- 260.csv
- 260.tif
- 264.csv
- 264.tif
- 272.csv
- 272.tif
- 281.csv
- 281.tif
- 296.csv
- 296.tif
- 29.csv
- 29.tif
- 313.csv
- 313.tif
- 315.csv
- 315.tif
- 31.csv
- 31.tif
- 320.csv
- 320.tif
- 343.csv
- 343.tif
- 349.csv
- 349.tif
- 359.csv
- 359.tif
- 361.csv
- 361.tif
- 364.csv
- 364.tif
- 385.csv
- 385.tif
- 397.csv
- 397.tif
- 399.csv
- 399.tif
- 400.csv
- 400.tif
- 405.csv
- 405.tif
- 409.csv
- 409.tif
- 43.csv
- 43.tif
- 446.csv
- 446.tif
- 449.csv
- 449.tif
- 457.csv
- 457.tif
- 464.csv
- 464.tif
- 485.csv
- 485.tif
- 500.csv
- 500.tif
- 504.csv
- 504.tif
- 506.csv
- 506.tif
- 514.csv
- 514.tif
- 529.csv
- 529.tif
- 541.csv
- 541.tif
- 61.csv
- 61.tif
- 64.csv
- 64.tif
- 663.csv
- 663.tif
- 67.csv
- 67.tif
- 705.csv
- 705.tif
- 79.csv
- 79.tif
- 82.csv
- 82.tif
- 8.csv
- 8.tif
- PHH3/
- 108.csv
- 108.tif
- 128.csv
- 128.tif
- 147.csv
- 147.tif
- 155.csv
- 155.tif
- 157.csv
- 157.tif
- 158.csv
- 158.tif
- 168.csv
- 168.tif
- 172.csv
- 172.tif
- 208.csv
- 208.tif
- 237.csv
- 237.tif
- 241.csv
- 241.tif
- 244.csv
- 244.tif
- 245.csv
- 245.tif
- 260.csv
- 260.tif
- 264.csv
- 264.tif
- 272.csv
- 272.tif
- 281.csv
- 281.tif
- 296.csv
- 296.tif
- 29.csv
- 29.tif
- 313.csv
- 313.tif
- 315.csv
- 315.tif
- 31.csv
- 31.tif
- 320.csv
- 320.tif
- 343.csv
- 343.tif
- 349.csv
- 349.tif
- 359.csv
- 359.tif
- 361.csv
- 361.tif
- 364.csv
- 364.tif
- 385.csv
- 385.tif
- 397.csv
- 397.tif
- 399.csv
- 399.tif
- 400.csv
- 400.tif
- 405.csv
- 405.tif
- 409.csv
- 409.tif
- 43.csv
- 43.tif
- 446.csv
- 446.tif
- 449.csv
- 449.tif
- 457.csv
- 457.tif
- 464.csv
- 464.tif
- 485.csv
- 485.tif
- 500.csv
- 500.tif
- 504.csv
- 504.tif
- 506.csv
- 506.tif
- 514.csv
- 514.tif
- 529.csv
- 529.tif
- 541.csv
- 541.tif
- 61.csv
- 61.tif
- 64.csv
- 64.tif
- 663.csv
- 663.tif
- 67.csv
- 67.tif
- 705.csv
- 705.tif
- 79.csv
- 79.tif
- 82.csv
- 82.tif
- 8.csv
- 8.tif