G banded metaphase images

Published: 23 August 2021| Version 1 | DOI: 10.17632/nn4353y2xx.1
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Description

Access to datasets is vital to research, design and development of machine learning models and algorithms. Machine learning approaches for automated karyotyping system always require metaphase image dataset. The human metaphase images are not easily available for the researches in the field of cytogenetics. With the present contribution, microscopic images of G banded human metaphases are provided and made publicly available to research community. The dataset is prepared from the peripheral blood samples collected from volunteers. Through a series of cytogenetic procedures namely, culturing, harvesting, slide preparation, banding and staining , G banded metaphase images are captured using Leica DM 2500 microscope and Leica DMC 2900 camera. These image data can be used by the researchers basically for automated karyotyping system design and research. Researchers in various image processing and machine learning applications fields such as preprocessing, segmentation, metaphase classification can make use of these images. There are 100 sample images with resolution 2048 * 1536 and bit depth 24 are provided. All images are in .png format.

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Steps to reproduce

The following are the main steps in the cytogenetic procedure for slide preparation and image collection for the dataset “ G banded human metaphase images” • Add Eight drops of the peripheral blood to 8 ml supplemented media. • Add 80µl freshly diluted PHA to the culture. • Incubate for 72 hours at 37ºC. • Add colchicine (80 µl) at the 69th hour. • After incubation, take out the culture tube and centrifuge for 10 min at 800-1000rpm. • Discard the supernatant by pipetting out the media, leaving as little media as possible over the button. • Resuspend the cell button in 10ml of hypotonic solution (0.075M KCl) and incubate for 15 - 20 minutes at 37° C (hypotonic solution should be pre-warmed to 37° C before use). • After the hypotonic treatment, add 5 drops of freshly made fixative to the tube and mix gently by inverting the tube once or twice. Then keep the tube at room temperature for 5-10 minutes. (Note: Cells should be handled very gently following hypotonic treatment. Any harsh treatment may rupture the cells, leading to many undesirable incomplete metaphases in final preparation). • Now, centrifuge the tubes at 800-1000 rpm for 10 minutes. • After centrifugation, discard the supernatant and mix the pellet thoroughly in 10ml of fixative (without pipetting) and keep the solution at 4°C overnight for fixation. • After overnight fixation, centrifuge the tubes at 800-1000 rpm for 10 minutes, discard the supernatant and resuspend the cells in fresh fixative. Repeat this step 3 times (till the pellet becomes white in color). • Preparing sample for slide preparation- After the final centrifugation, resuspend the cells in a small volume of fixative approximately 0.5 to 1ml, (depending on the size of the cell button) to give a slightly opaque suspension. Slide preparation • Drop the cell suspension (3-4 drops) from a height evenly on a cold, wet slide and allow to dry at room temperature (or heat fix at 69-720C). • Age the air dried slide over night at 55°C to 60°C in an oven. • Treat the slides in Trypsin solution for 5-10 seconds. • Rinse the slides briefly in cold Sorrensen's Buffer (2-5° C, kept in refrigerator). • Stain the treated slides in Giemsa staining solution for 4-6 minutes. • Rinse in distilled water and allowed to dry. • The slides are observed without mounting using dry objectives. If satisfactory, they are examined under oil immersion objective. • Select Region of Interest (ROI) using image capturing system of microscopic camera (Here, Leica 2900 DMC attached to microscope DM2900 is used)

Institutions

Regional Cancer Centre Thiruvananthapuram, College of Engineering Karunagappally

Categories

Computer Science Applications, Computer Engineering, Cell Genetics, Chromosome Analysis

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