Jumping from raw data to image analysis

Biological images contain huge amounts of information, and processing it during analysis of the results is often the bottleneck in research. Imaging and image analysis expert Ilya Belevich has developed open-source software that makes life easier for himself and other researchers.

Years of working with imaging at the University of Helsinki have familiarised Ilya Belevich from the Electron Microscopy Unit of the Institute of Biotechnology with both hardware and software in the field. The content of a typical workday for the MSc from the Lomonosov Moscow State University and PhD from the University of Helsinki may, of course, vary, but consists mainly of imaging needed for different projects, analysis of electron or light microscopy images or the development of software suited to those needs.

The main goal is to image and analyse the samples so that the results reflect the reality as closely as possible.

“Well, I must admit that I began developing software mainly because I wanted to make my life easier,” laughs Ilya Belevich.


MIB helps to analyse multidimensional image data

In addition to making small tweaks in the already existing imaging software, Ilya Belevich has developed open-source software called the Microscopy Image Browser (MIB).

Originally, the MIB was intended to be a just a simple image viewer. However, it has now become a package designed to easily segment and analyse rather large multidimensional datasets, such as those typically produced by both electron and light microscopy.

Ilya Belevich explains: “Biological imaging usually produces plain 2D images that are sometimes difficult to interpret. For example, whether a circular profile on the image is in reality a tube or part of a sphere may be unclear. To answer such questions, the researcher must either perform a thorough analysis of many plain images or jump into the world of 3D imaging. The resulting 3D datasets may be further segmented to in order to extract the exact shapes and properties of objects of interest. That’s where MIB comes in handy.”

Even in the most common, plain biological images contain a lot of information that needs to be extracted for analysis.

“Biologists want to know how their research subject works, but sometimes they are somewhat unsure how to extract the required information from the raw images so that they can analyse it. In such situations, I try to help them by suggesting possible solutions or by developing and implementing some specific project-targeted routines,” Ilya Belevich says.


Ways of developing software differ

Both commercial and free image analysis software is available, but both have their downsides.

“Commercial programs are generally intended only for specific purposes and are difficult to adjust to meet the needs of a particular research project. And, of course, you must pay for them. On the other hand, the free software may not be very versatile or user-friendly. Luckily, some of the free programs are distributed under the open-source license, which makes it easier to create discussions, to collaborate and to shape the software to meet all kinds of needs,” Ilya Belevich notes.

Ilya Belevich believes that the development of the programs also differs.

“A computer company may havea clear task in mind. They define in advance all the required parameters for the program. During the research, we often have no clear plan, because we are not yet sure what kind of results or type of data we will be dealing with next month, much less next year. Things are changing quite fast even within the same research project,” Ilya Belevich says.