arXiv subjects

Sebastian Berisha

Publications and source records attributed to Sebastian Berisha.

4 recordsLinked to original sources

arXiv2024

Rapid hyperspectral photothermal mid-infrared spectroscopic imaging from sparse data for gynecologic cancer tissue subtyping

Ovarian cancer detection has traditionally relied on a multi-step process that includes biopsy, tissue staining, and morphological analysis by experienced pathologists. While widely practiced, this conventional approach suffers from several drawbacks: it is qualitative, time-intensive, and heavily dependent on the quality of staining. Mid-infrared (MIR) hyperspectral photothermal imaging is a label-free, biochemically quantitative technology that, when combined with machine learning algorithms, can eliminate the need for staining and provide quantitative results comparable to traditional histology. However, this technology is slow. This work presents a novel approach to MIR photothermal imaging that enhances its speed by an order of magnitude. Our method significantly accelerates data collection by capturing a combination of high-resolution and interleaved, lower-resolution infrared band images and applying computational techniques for data interpolation. We effectively minimize data collection requirements by leveraging sparse data acquisition and employing curvelet-based reconstruction algorithms. This method enables the reconstruction of high-quality, high-resolution images from undersampled datasets and achieving a 10X improvement in data acquisition time. We assessed the performance of our sparse imaging methodology using a variety of quantitative metrics, including mean squared error (MSE), structural similarity index (SSIM), and tissue subtype classification accuracies, employing both random forest and convolutional neural network (CNN) models, accompanied by ROC curves. Our statistically robust analysis, based on data from 100 ovarian cancer patient samples and over 65 million data points, demonstrates the method's capability to produce superior image quality and accurately distinguish between different gynecological tissue types with segmentation accuracy exceeding 95%.

cs.CV↗

arXiv2022

Adaptive Compressive Sampling for Mid-infrared Spectroscopic Imaging

Minfrared spectroscopic imaging (MIRSI) is an emerging class of label-free, biochemically quantitative technologies targeting digital histopathology. Conventional histopathology relies on chemical stains that alter tissue color. This approach is qualitative, often making histopathologic examination subjective and difficult to quantify. MIRSI addresses these challenges through quantitative and repeatable imaging that leverages native molecular contrast. Fourier transform infrared (FTIR) imaging, the best-known MIRSI technology, has two challenges that have hindered its widespread adoption: data collection speed and spatial resolution. Recent technological breakthroughs, such as photothermal MIRSI, provide an order of magnitude improvement in spatial resolution. However, this comes at the cost of acquisition speed, which is impractical for clinical tissue samples. This paper introduces an adaptive compressive sampling technique to reduce hyperspectral data acquisition time by an order of magnitude by leveraging spectral and spatial sparsity. This method identifies the most informative spatial and spectral features, integrates a fast tensor completion algorithm to reconstruct megapixel-scale images, and demonstrates speed advantages over FTIR imaging while providing spatial resolutions comparable to new photothermal approaches.

eess.IV↗

arXiv2022

Leveraging mid-infrared spectroscopic imaging and deep learning for tissue subtype classification in ovarian cancer

Mid-infrared spectroscopic imaging (MIRSI) is an emerging class of label-free techniques being leveraged for digital histopathology. Modern histopathologic identification of ovarian cancer involves tissue staining followed by morphological pattern recognition. This process is time-consuming, subjective, and requires extensive expertise. This paper presents the first label-free, quantitative, and automated histological recognition of ovarian tissue subtypes using a new MIRSI technique. This technique, called optical photothermal infrared (O-PTIR) imaging, provides a 10X enhancement in spatial resolution relative to prior instruments. It enables sub-cellular spectroscopic investigation of tissue at biochemically important fingerprint wavelengths. We demonstrate that enhanced resolution of sub-cellular features, combined with spectroscopic information, enables reliable classification of ovarian cell subtypes achieving a classification accuracy of 0.98. Moreover, we present statistically robust validation from 74 patient samples with over 60 million data points. We show that sub-cellular resolution from five wavenumbers is sufficient to outperform state-of-the-art diffraction-limited techniques from up to 235 wavenumbers. We also propose two quantitative biomarkers based on the relative quantities of epithelium and stroma that exhibits efficacy in early cancer diagnosis. This paper demonstrates that combining deep learning with intrinsic biochemical MIRSI measurements enables quantitative evaluation of cancerous tissue, improving the rigor and reproducibility of histopathology.

q-bio.TO↗

arXiv2018

Three-Dimensional GPU-Accelerated Active Contours for Automated Localization of Cells in Large Images

Cell segmentation in microscopy is a challenging problem, since cells are often asymmetric and densely packed. This becomes particularly challenging for extremely large images, since manual intervention and processing time can make segmentation intractable. In this paper, we present an efficient and highly parallel formulation for symmetric three-dimensional (3D) contour evolution that extends previous work on fast two-dimensional active contours. We provide a formulation for optimization on 3D images, as well as a strategy for accelerating computation on consumer graphics hardware. The proposed software takes advantage of Monte-Carlo sampling schemes in order to speed up convergence and reduce thread divergence. Experimental results show that this method provides superior performance for large 2D and 3D cell segmentation tasks when compared to existing methods on large 3D brain images.

eess.IV↗