A.M. Lyakh, T.V. Rauen, V.S. Mukhanov
A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS
RF, Sevastopol, Nakhimov Av., 2
The trajectories of microorganism movements are one of the most accessible sources of data on their response to external conditions. Trajectories are studied using video records. Specialized tracking software processes the video material and builds trajectories, and we use mathematical methods to analyze trajectory characteristics and make conclusions about the dependence of microorganism movement patterns on the surrounding conditions.
In this way, we make an attempt to identify the relationship between the movement patterns of the microscopic heterotrophic dinoflagellates Oxyrrhis marina and the presence or absence of available food. Unfortunately, video of the microorganism movements appears to be low-contrast and tracking programs are not able to correctly identify moving objects. Due to this reason, a script has been written to improve the visibility of moving objects. For that purpose, the script converts video to black and white (binary) format. With the help of FFmpeg the script cuts out video frames and, using ImageMagick, automatically processes them into binary format.
As a result, the following sequence of ImageMagick commands produces high-quality binary frames: get source frame → extract red channel (-channel r -separate) → stretch histogram (-auto-level) → correct black and white levels and gamma (-level 70%,100%,3) → blurring (-blur 30) > negate (-negate) → use adaptive local thresholding (-lat 30×30+5%).
The command sequence is written as an algorithm in the Windows batch file that allows any researcher to automatically improve the quality of video recordings and prepare them for subsequent extraction of the microorganism trajectories.
Keywords: digital image processing, trajectories of movement, histogram correction, local adaptive thresholding.
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