Biology subjects

Rogalski, M.

Publications and source records attributed to Rogalski, M..

4 recordsLinked to original sources

bioRxiv2026

Doubling the Field of View in Common-Path Digital Holographic Microscopy via Wavelength Scanning and Polarization Gratings

Digital holographic microscopy systems in a common-path configuration, compared to systems with a separate reference arm, offer a compact design and resistance to disturbances. They can operate with partially coherent illumination, reducing speckle noise. However, they are limited by the overlapping of the object beam and its laterally shifted replica. As a result, images from different regions of the object overlap on the detector, preventing imaging of dense samples. We present the wavelength-scanning replica-removal method, which solves this problem by enabling the separation of information from both replicas and thereby doubling the effective field of view (FOV). The wavelength-scanning multi-shear replica removal algorithm plays a key role in reconstructing the undisturbed phase from a series of holograms recorded with variable shears. The shear value is controlled by changing the illumination wavelength. This enabled the development of two measurement modes: time-domain wavelength scanning for high-quality imaging, and a single-shot mode with frame division into color channels to improve temporal resolution. The method was validated using resolution tests and biological samples - neurons and dynamic yeast cultures. By combining the advantages of the common-path configuration with dense-structure imaging and dynamic processes, the proposed method constitutes a versatile tool for quantitative phase microscopy.

biophysics↗

bioRxiv2025

Atypical plastid genome evolution: Cereus Mill. from distinct environments harbor one of the largest plastid genomes in Cactaceae

BackgroundCactaceae has successfully radiated in xeric habitats across the Americas, presenting very distinct morphologies and evolutionary patterns within tribes. This study presents the complete plastomes of C. jamacaru subsp. jamacaru and C. hildmannianus subsp. hildmannianus, which inhabit distinct habitats, providing insights into their genomic structure and evolutionary history, with implications for conservation. Methods and ResultsChloroplast genomes of the two Cereus were assembled and analyzed to investigate plastome evolution in Cactoideae. Fresh cladodes were collected and their mesophyll manually extracted, chloroplasts were extracted from the mesophyll, and cpDNA sequenced using Illumina MiSeq. De novo assembly and annotation were conducted using BLAST, Expasy, and tRNAScan as validation tools. We compared the genome structure, gene content, codon usage, and RNA editing predictions between tribes. The genome was 141.884 and 141.600 bp for C. jamacaru and C. hildmannianus, respectively, and dotplot analysis confirmed highly syntenic plastomes. The genes trnV-GAC, trnV-UAC, rpl23, ndhA, ndhE, ndhG, ndhI, and ndhK were lost, and ndhB, ndhC, ndhF, and rpl33 are pseudogenes. The tRNAval losses indicate putative superwobbling or nuclear-coded tRNA import from cytosol. We identified an insertion in rps18 for both Cereus, suggesting that intron retention may be in course for these species. We identified [~]190 single sequence repeats and 50 tandem repeats for each species, and eight exclusive RNA editing sites. Synteny analysis revealed rearrangements distinguishing taxa within Cactoideae. Phylogenetic results supported Cereus monophyly, corroborating existing classifications, and clarifies unresolved relationships, enhancing understanding of phylogenetic relationships within Cactaceae. ConclusionsOur results provide evidence on the evolutionary patterns and putative signatures of adaptation to distinct environments, providing insights into genomic evolution and conservation of Cereus.

evolutionary biology↗

bioRxiv2024

Polarization gratings aided common-path Hilbert holotomography for high-throughput lipid droplets content assay

In this contribution we present a novel polarization gratings aided common-path Hilbert holotomography (CP-HHT) for high-throughput 3D refractive index imaging. Addressing limitations in current holotomography methods, we leverage the extended space-bandwidth product (SBP) through robust phase demodulation using Hilbert spiral transform. Thanks to the application of polarization diffraction gratings our system enables fully tailored holographic settings such as fringe density and shear, thus allowing flexible hologram demodulation, while maintaining simplicity and robustness. The performance is tested on a 3D-printed (using two-photon polymerization) brain phantom and fixed HeLa cells supplemented with cholesterol and oleic acids. Reconstruction analysis using the brain phantom indicates that the Hilbert method provides comparable results and resolution to the Fourier transform method in a significantly expanded measurement throughput. Our CP-HHT approach demonstrates the unique (not possible by fluorescence) high-throughput (especially when compared to cryogenic electron microscopy) capability to differentiate between cholesterol esters vs. triacylglycerol (TAG) rich lipid droplets (LDs), thus has potential for label-free biological research at sub-cellular level. The quantitative analysis of LDs refractive index emphasizes the methods sensitivity in distinguishing between LDs with different neutral lipid content, offering new insights into LD heterogeneity, thus reinforcing the versatility and applicability of our CP-HHT system in broader bioimaging applications.

bioengineering↗

bioRxiv2021

FPM app: an open-source application for simple and intuitive Fourier ptychographic reconstruction

SummaryFourier ptychographic microscopy (FPM) is a computational microscopy technique that enables large field of view and high-resolution microscopic imaging of biological samples. However, the FPM does not yet have an adequately capable open-source software. In order to fill this gap we are presenting novel, simple, universal, semi-automatic and highly intuitive graphical user interface (GUI) open-source application called the FPM app enabling wide-scale robust FPM reconstruction. Apart from implementing the FPM in accessible GUI app, we also made several improvements in the FPM image reconstruction process itself, making the FPM more automatic, noise-robust and faster. Availability and ImplementationFPM app was implemented in MATLAB and all MATLAB codes along with standalone executable version of the FPM app and the online documentation are freely accessible at https://github.com/MRogalski96/FPM-app. Our exemplary FPM datasets may be downloaded at https://bit.ly/2MxNpGb.

bioinformatics↗