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Data from: Spectroscopic approach to correction and visualisation of bright-field light transmission microscopy biological data

Citation

Platonova, Ganna et al. (2021), Data from: Spectroscopic approach to correction and visualisation of bright-field light transmission microscopy biological data, Dryad, Dataset, https://doi.org/10.5061/dryad.63xsj3v2d

Abstract

The most realistic information about the transparent sample such as a live cell can be obtained only using bright-field light microscopy. At high-intensity pulsing LED illumination, we captured a primary 12-bit-per-channel (bpc) response from an observed sample using a bright-field wide-field microscope equipped with a high-resolution (4872x3248) image sensor. In order to suppress data distortions originating from the light interactions with undesirable elements in the optical path, poor sensor reproduction (geometrical defects of the camera sensor and some peculiarities of sensor sensitivity), this uncompressed 12-bpc data underwent a kind of correction after simultaneous calibration of all the parts of the experimental arrangement. Moreover, the final intensities of the corrected images are proportional to the photon fluxes detected by a camera sensor. It can be visualized in 8-bpc intensity depth after the Least Information Loss compression [Lect. Notes Bioinform. 9656, 527 (2016)].

Methods

The raw images in "SupplFigs.pdf" were obtained using a nanoscope (bright-field wide-field video-enhancenced photon microscope developed for Institute of Complex Systems in Nové Hrady). These raw images were calibrated by the relevant calibration files (in the "calib_sets" folder) obtained by the nanoscope and an optical fiber spectrophotometer using a VerCa software (available upon request). The "scripts" folder contains Matlab scripts for further image processing, image analysis and drawing graphs.

In the "calib_sets" folder, you can find a README.txt with the description of the subfolders' contents. In the "scripts" folder, the Matlab scripts are divided into subfolders according to the figures' labels in the paper.

Funding

Ministerstvo Školství, Mládeže a Tělovýchovy, Award: CENAKVA LM2018099

European Regional Development Fund, Award: Image Headstart ATCZ215: Interreg V-A Austria–Czech Republic

GAJU, Award: 017/2016/Z

Charles University, Award: UNCE/SCI/010