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BioMediTech RPE dataset

dataset
posted on 2016-02-04, 11:41 authored by Florentino SantosFlorentino Santos
--BioMediTech RPE dataset--

(Further detailed explanation provided inside the archive)

RPE dataset for the article:
- L. Nanni, M. Paci, F. L. C. Santos, H. Skottman, K. Juuti-Uusitalo, J. Hyttinen, Texture descriptors ensembles enable image-based classification of maturation of human stem cell-derived retinal pigmented epithelium, Plos One 2016


Image acquisition

Each RPE cell culture was imaged with the same settings. The microscope used was a Nikon Eclipse TE200S phase-contrast microscope (Nikon Instruments Europe B.V., Amstelveen, Netherlands) with the 20x objective and Ph1 phase contrast. 

Cell imaging parameters are the following:
- Quality 2560 x 1920 pixels
- Mode Manual exposure
- Exposure 25 – 125 ms
- AE compensation 0
- Gain 1.2 x
- Contrast Dynamic

Subwindows dividing process

The dataset is composed of 195 images that were divided into 16 subwindows and each subwindow labeled into 4 classes by two trained operators. Every subwindow that presented clutters, out of focus elements or just background was discarded and is not part of this dataset.

Subwindows coding

Each subwindow was renamed after manual classification using a specific code. This code was assembled by five elements: 
(initial image classification)_( image number)_(subwindow number)_(subwindow classification)_(inclusion bit).tif

Classification criteria

The full dataset is composed of 1862 subwindows. The subwindows classification used the following parameters:

Fusiform (216 images)
-Fuse shaped cell contours and nucleus
-Separated cells

Epithelioid (547 images)
-Globular shaped cell contours and nucleus
-More packed

Cobblestone (949 images)
-Well defined cell contours and cell wall
-Hexagonal shape
-Homogeneous cytoplasm
-Tightly packed

Mixed (150 images)
-Two or more of afore mentioned classes

Dataset file structure

RPE_dataset.zip
├ Description.pdf
Description of the acquisition, creation and structure of the dataset.
├ Images
Initial images (RPE cell culture)
├ Subwindows
Subwindows from the division of the initial images.          Coded as mentioned in Subwindows coding
├ license.txt
The Creative Common Attribution 4.0. license

History