[HTML][HTML] Data-analysis strategies for image-based cell profiling

JC Caicedo, S Cooper, F Heigwer, S Warchal, P Qiu… - Nature …, 2017 - nature.com
Image-based cell profiling is a high-throughput strategy for the quantification of phenotypic
differences among a variety of cell populations. It paves the way to studying biological …

[HTML][HTML] nucleAIzer: a parameter-free deep learning framework for nucleus segmentation using image style transfer

R Hollandi, A Szkalisity, T Toth, E Tasnadi, C Molnar… - Cell systems, 2020 - cell.com
Single-cell segmentation is typically a crucial task of image-based cellular analysis. We
present nucleAIzer, a deep-learning approach aiming toward a truly general method for …

Evaluation of deep learning strategies for nucleus segmentation in fluorescence images

JC Caicedo, J Roth, A Goodman, T Becker… - Cytometry Part …, 2019 - Wiley Online Library
Identifying nuclei is often a critical first step in analyzing microscopy images of cells and
classical image processing algorithms are most commonly used for this task. Recent …

[HTML][HTML] Test-time augmentation for deep learning-based cell segmentation on microscopy images

N Moshkov, B Mathe, A Kertesz-Farkas, R Hollandi… - Scientific reports, 2020 - nature.com
Recent advancements in deep learning have revolutionized the way microscopy images of
cells are processed. Deep learning network architectures have a large number of …

[HTML][HTML] DeepSynth: Three-dimensional nuclear segmentation of biological images using neural networks trained with synthetic data

KW Dunn, C Fu, DJ Ho, S Lee, S Han, P Salama… - Scientific reports, 2019 - nature.com
The scale of biological microscopy has increased dramatically over the past ten years, with
the development of new modalities supporting collection of high-resolution fluorescence …

[HTML][HTML] Systems pathology by multiplexed immunohistochemistry and whole-slide digital image analysis

S Blom, L Paavolainen, D Bychkov, R Turkki… - Scientific reports, 2017 - nature.com
The paradigm of molecular histopathology is shifting from a single-marker
immunohistochemistry towards multiplexed detection of markers to better understand the …

[HTML][HTML] Tertiary lymphoid structures (TLS) identification and density assessment on H&E-stained digital slides of lung cancer

P Barmpoutis, M Di Capite, H Kayhanian… - Plos one, 2021 - journals.plos.org
Tertiary lymphoid structures (TLS) are ectopic aggregates of lymphoid cells in inflamed,
infected, or tumoral tissues that are easily recognized on an H&E histology slide as discrete …

Seens: Nuclei segmentation in pap smear images with selective edge enhancement

M Zhao, H Wang, Y Han, X Wang, HN Dai… - Future Generation …, 2021 - Elsevier
Accurate nuclei segmentation, as an indispensable basis and core link for multi-cell cervical
image analysis, plays an important role in automatic pre-cancer detection. However, poor …

Image analyses for engineering advanced tissue biomanufacturing processes

MC Allenby, MA Woodruff - Biomaterials, 2022 - Elsevier
Industrial cell culture processes are inherently expensive, time-consuming, and variable.
These limitations have become a critical bottleneck for the industrial translation of human …

[HTML][HTML] Establishment of a morphological atlas of the Caenorhabditis elegans embryo using deep-learning-based 4D segmentation

J Cao, G Guan, VWS Ho, MK Wong, LY Chan… - Nature …, 2020 - nature.com
The invariant development and transparent body of the nematode Caenorhabditis elegans
enables complete delineation of cell lineages throughout development. Despite extensive …