Development of a software package for processing microscopic images of focal adhesions

Project title:

Development of a software package for processing microscopic images of focal adhesions

IRN АР08053387

Aim of the project:

Development of a software package for fully automated processing of images of focal contacts, where microscopic images themselves will be at the input, and processed characteristics of biological objects will be obtained at the output

The relevance of research:

The development of machine processing methods in itself is vital today. Microscopes have now become the de facto standard tool in modern biology. A huge database of microscopic images has already been accumulated. However, due to the relative youth of this branch of science, there are very few software solutions related to automatic processing. Until recently, manual processing was also quite enough, but now it is already obvious that the amount of data already exceeds the limits of human capabilities. This is also aggravated by the fact that most of the processes in the cell are of an obvious stochastic nature. And it is impossible to simply measure the lifetime of an object, you need not only to measure the speed of several objects, but to have data from tens of thousands of objects so that you can reason at the level of distributions and statistics.

Expected results:

Cell lines will be obtained for imaging on a confocal microscope; Fluorescent vectors will be made for incorporation into cell lines; Fluorescent cell lines will be obtained; Carl Zeiss Cell Observer SD Confocal Microscope data will be collected; Microscopic images from culture cells will be collected; Processed images will be obtained; Post Processing programs will be developed; The functions of the focal contact intensity versus time will be found; Images will be sorted by intensity function and plotting distributions

Obtained results:

During the period of work in 2020-2021, culture cell lines of the HeLa S3 type were grown for visualization on a confocal microscope. Also, vectors were designed to introduce HeLa S3 cell lines. Work was carried out to optimize vectors and cell cultures for further analysis of focal contacts in culture models of cells of epithelial origin. The analysis of the expression of the constructed vectors was carried out. Also, cultured cells were grown for transfection of fluorescent vectors. A software block was developed for primary image processing using Fourier filtering in two dimensions. Based on the results of the study, an abstract was published at an international conference on the theme "Molecules of Life: Towards New Horizons" at the International Congress on Biochemistry and Molecular Biology in Ljubljana, Slovenia. In 2021. within the framework of the project, all the studies carried out were fully carried out in accordance with the project schedule. A software block for primary image processing was developed. According to the results of the study, two scientific articles were published in the international scientific journal "Frontiers in Cell and Developmental Biology" with an impact factor of 5.87.

Research group

Principal investigator:

 Urazbaev Arshat Orynbasarovich, PhD, Researcher, work experience: computer simulation of plasma turbulence, digital signal processing and biological image processing.

Scopus ID: 8925454800


Baiken Yeldar, MSc, Researcher, PhD student, work experience in cell biology, flow cytometry, imaging, biochemistry, confocal microscopy and DNA repair.

Scopus ID: 55573387800


Ashimova Assem, MSc, Junior Researcher, PhD student with experience in cell biology, molecular biology and immunology.


Zhulamanova Ainur, MSc, research assistant, experience in cell biology, molecular biology, microbiology and virology.

External collaborator:

Yegorov Sergey, PhD, Researcher, work experience and research in immunology, bioinformatics and biostatistics.

Scopus ID: 26434035900



  1. Baiken Y, Kanayeva D, Taipakova S, Groisman R, Ishchenko AA, Begimbetova D, Matkarimov B, Saparbaev M. Role of Base Excision Repair Pathway in the Processing of Complex DNA Damage Generated by Oxidative Stress and Anticancer Drugs. Front Cell Dev Biol. 2021 Jan 22;8:617884. doi: 10.3389/fcell.2020.617884. PMID: 33553154; PMCID: PMC7862338.
  2. 2. Kauanova S, Urazbayev A, Vorobjev I. The Frequent Sampling of Wound Scratch Assay Reveals the "Opportunity" Window for Quantitative Evaluation of Cell Motility-Impeding Drugs. Front Cell Dev Biol. 2021 Mar 11;9:640972. doi: 10.3389/fcell.2021.640972. PMID: 33777948; PMCID: PMC7991799.
  3. 3. Baiken, Y., Kanayeva, D., Zhulamanova, A., Matkarimov, B., Groisman, R., & Saparbaev, M. (2021, July). Study of the role human NEIL3 DNA glycosylase in the repair of cisplatin DNA damage in HeLa S3 cells. In FEBS OPEN BIO (Vol. 11, pp. 419-419). 111 RIVER ST, HOBOKEN 07030-5774, NJ USA: WILEY.