[HTML][HTML] Computational pathology: a survey review and the way forward

MS Hosseini, BE Bejnordi, VQH Trinh, L Chan… - Journal of Pathology …, 2024 - Elsevier
Abstract Computational Pathology (CPath) is an interdisciplinary science that augments
developments of computational approaches to analyze and model medical histopathology …

Nucleus segmentation: towards automated solutions

R Hollandi, N Moshkov, L Paavolainen, E Tasnadi… - Trends in Cell …, 2022 - cell.com
Single nucleus segmentation is a frequent challenge of microscopy image processing, since
it is the first step of many quantitative data analysis pipelines. The quality of tracking single …

Democratising deep learning for microscopy with ZeroCostDL4Mic

L von Chamier, RF Laine, J Jukkala, C Spahn… - Nature …, 2021 - nature.com
Deep Learning (DL) methods are powerful analytical tools for microscopy and can
outperform conventional image processing pipelines. Despite the enthusiasm and …

Deep Visual Proteomics defines single-cell identity and heterogeneity

A Mund, F Coscia, A Kriston, R Hollandi… - Nature …, 2022 - nature.com
Despite the availabilty of imaging-based and mass-spectrometry-based methods for spatial
proteomics, a key challenge remains connecting images with single-cell-resolution protein …

Advances and opportunities in image analysis of bacterial cells and communities

H Jeckel, K Drescher - FEMS Microbiology Reviews, 2021 - academic.oup.com
The cellular morphology and sub-cellular spatial structure critically influence the function of
microbial cells. Similarly, the spatial arrangement of genotypes and phenotypes in microbial …

Nuinsseg: a fully annotated dataset for nuclei instance segmentation in h&e-stained histological images

A Mahbod, C Polak, K Feldmann, R Khan, K Gelles… - Scientific Data, 2024 - nature.com
In computational pathology, automatic nuclei instance segmentation plays an essential role
in whole slide image analysis. While many computerized approaches have been proposed …

Deep learning for bioimage analysis in developmental biology

A Hallou, HG Yevick, B Dumitrascu… - Development, 2021 - journals.biologists.com
Deep learning has transformed the way large and complex image datasets can be
processed, resha** what is possible in bioimage analysis. As the complexity and size of …

Nisnet3d: Three-dimensional nuclear synthesis and instance segmentation for fluorescence microscopy images

L Wu, A Chen, P Salama, S Winfree, KW Dunn… - Scientific Reports, 2023 - nature.com
The primary step in tissue cytometry is the automated distinction of individual cells
(segmentation). Since cell borders are seldom labeled, cells are generally segmented by …

Label-free live cell recognition and tracking for biological discoveries and translational applications

B Chen, Z Yin, BWL Ng, DM Wang, RS Tuan, R Bise… - npj Imaging, 2024 - nature.com
Label-free, live cell recognition (ie instance segmentation) and tracking using computer
vision-aided recognition can be a powerful tool that rapidly generates multi-modal readouts …

EXACT: a collaboration toolset for algorithm-aided annotation of images with annotation version control

C Marzahl, M Aubreville, CA Bertram, J Maier… - Scientific reports, 2021 - nature.com
In many research areas, scientific progress is accelerated by multidisciplinary access to
image data and their interdisciplinary annotation. However, kee** track of these …