PATH-DT-MSU Dataset

Description

Real biopsy and surgical material from various parts of the human digestive tract was used for paraffin blocks preparation. Microscopic examination was performed using microscope Leica DM2500 (Leica Microsystems, Germany). Microscope Leica DM4000B/DFC495 and scanner Leica SCN400 (Leica Microsystems, Germany) were used for high resolution histological images acquisition.

source imagevisualization of gland and "open" gland annotations

PATH-DT-MSU dataset was created to unite high-quality histological images of different parts of human gastrointestinal tract and consists of several sets:

  • S1: histological images of colon;
  • S2: histological images of stomach (coming soon);
  • S3: histological images of esophagus (coming soon)

All images are provided with pixel-level instance annotations. All images for convenience are already split into train and test samples.

Versioning system

PATH-DT-MSU is actively updated and expanded so for convenient usage each set supports versioning system. Every new version of set besides offering new images will contain all images from the previous version. Image annotations (including the number of supported classes of histological structures) can be modified and expanded from version to version. All outdated versions as well as the latest one are available for download.

Summary

settissueversionnumber of images [train/test]number of classesmagnitudeimage sizes in pixelsrelease datedownload
S1colonv280 [40/40]2x103263 x 2442,
2176 x 1632
18.08.2019link
v120 [10/10]2x102176 x 163207.06.2019link

Directory structure

The dataset is organised in sets and samples (train/test). Every source image is accompanied with annotation images (..._anno_c1.png, ...anno_c2.png, ...), each of them contains instance pixel-level segmentation of corresponding type of histological structure. The description of annotated classes of histological structures for each set can be found in anno.xls table. Short medical description of each image from the set can be found in description.xls table.

PATH-DT-MSU
|- S1
|   |- v1
|   |   |- anno.xls
|   |   |- description.xls
|   |   |- test
|   |   |   |- s1_test_01.png
|   |   |   |- s1_test_01_anno_c1.png
|   |   |   |- s1_test_01_anno_c2.png
|   |   |   | ...
|   |   |   |- s1_test_10.png
|   |   |   |- s1_test_10_anno_c1.png
|   |   |   |- s1_test_10_anno_c2.png
|   |   |- train
|   |   |   |- s1_train_01.png
|   |   |   |- s1_train_01_anno_c1.png
|   |   |   |- s1_train_01_anno_c2.png
|   |   |   | ...
|   |   |   |- s1_train_10.png
|   |   |   |- s1_train_10_anno_c1.png
|   |   |   |- s1_train_10_anno_c2.png
|   |- v2
|   |   |- anno.xls
|   |   |- description.xls
|   |   |- train
|   |   |   | ...
|   |   |- test
|   |   |   | ...
|- S2
|   |- v1
|   |   | ...
|   | ...
| ...

Our team

PATH-DT-MSU dataset was collected, prepared and annotated by Laboratory of Mathematical Methods of Image Processing, Faculty of Computational Mathematics and Cybernetics, Lomonosov Moscow State University and Department of Pathology, Medical Research and Educational Center (University Clinic), Lomonosov Moscow State University:

Alexander Khvostikov
khvostikov@cs.msu.ru
ORCID: 0000-0002-4217-7141
Laboratory of Mathematical Methods of Image Processing, Faculty of Computational Mathematics and Cybernetics, Lomonosov Moscow State University

Andrey Krylov
kryl@cs.msu.ru
ORCID: 0000-0001-9910-4501
Professor, Head of the Laboratory of Mathematical Methods of Image Processing, Faculty of Computational Mathematics and Cybernetics, Lomonosov Moscow State University

Ilya Mikhailov
imihailov@mc.msu.ru
ORCID: 0000-0001-8020-369X
Trainee researcher, Department of Pathology, Medical Research and Educational Center, Lomonosov Moscow State University.

Nina Oleynikova
noleynikova@mc.msu.ru
ORCID: 0000-0001-8564-8874
MD, PhD, Researcher scientist, Department of Pathology, Medical Research and Educational Center, Lomonosov Moscow State University.

Olga Kharlova
olga.arsenteva@gmail.com
ORCID: 0000-0002-5909-1248
MD, PhD

Natalia Danilova
ndanilova@mc.msu.ru
ORCID: 0000-0001-7848-6707
MD, PhD, Senior researcher scientist, Department of Pathology, Medical Research and Educational Center, Lomonosov Moscow State University.

Pavel Malkov
pmalkov@mc.msu.ru
ORCID: 0000-0001-5074-3513
MD, ScD, Head of Department of Pathology, Medical Research and Educational Center, Lomonosov Moscow State University.

Acknowledgement

The work was supported by Russian Science Foundation grant 17-11-01279.

Download the Dataset

Please download the required sets and versions of PATH-DT-MSU using the links from Summary section.
The latest version of PATH-DT-MSU dataset including all sets is available for download here.

Data Usage Agreement

You are free to use the provided data in your own research work. If you intend to publish research work that uses this dataset, you have to cite the references whenever appropriate.

Contact

For questions on PATH-DT-MSU dataset please contact Alexander Khvostikov: khvostikov@cs.msu.ru.

Bibliography

2019

A. Khvostikov, A. Krylov, I. Mikhailov, O. Kharlova, N. Oleynikova, P. Malkov. “Automatic mucous glands segmentation in histological images” // In: The International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences, Vol. XLII-2/W12. 2019, pp. 103−109. Link.

N. Oleynikova, A. Khvostikov, A. Krylov, I. Mikhailov, O. Kharlova, N. Danilova, P. Malkov, N. Ageykina, E. Fedorov. “Automatic glands segmentation in histological images obtained by endoscopic biopsy from various parts of the colon” // Endoscopy, Vol. 51(04), 2019, pp. 6−7. Link.