Image-based profiling for drug discovery: due for a machine-learning upgrade?

SN Chandrasekaran, H Ceulemans, JD Boyd… - Nature Reviews Drug …, 2021 - nature.com
Image-based profiling is a maturing strategy by which the rich information present in
biological images is reduced to a multidimensional profile, a collection of extracted image …

[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 …

Cellpose: a generalist algorithm for cellular segmentation

C Stringer, T Wang, M Michaelos, M Pachitariu - Nature methods, 2021 - nature.com
Many biological applications require the segmentation of cell bodies, membranes and nuclei
from microscopy images. Deep learning has enabled great progress on this problem, but …

Wilds: A benchmark of in-the-wild distribution shifts

PW Koh, S Sagawa, H Marklund… - International …, 2021 - proceedings.mlr.press
Distribution shifts—where the training distribution differs from the test distribution—can
substantially degrade the accuracy of machine learning (ML) systems deployed in the wild …

Cell detection with star-convex polygons

U Schmidt, M Weigert, C Broaddus, G Myers - Medical Image Computing …, 2018 - Springer
Automatic detection and segmentation of cells and nuclei in microscopy images is important
for many biological applications. Recent successful learning-based approaches include per …

High-speed fluorescence image–enabled cell sorting

D Schraivogel, TM Kuhn, B Rauscher… - Science, 2022 - science.org
Fast and selective isolation of single cells with unique spatial and morphological traits
remains a technical challenge. Here, we address this by establishing high-speed image …

Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl

JC Caicedo, A Goodman, KW Karhohs, BA Cimini… - Nature …, 2019 - nature.com
Segmenting the nuclei of cells in microscopy images is often the first step in the quantitative
analysis of imaging data for biological and biomedical applications. Many bioimage analysis …

Toward a foundation model of causal cell and tissue biology with a Perturbation Cell and Tissue Atlas

JE Rood, A Hupalowska, A Regev - Cell, 2024 - cell.com
Comprehensively charting the biologically causal circuits that govern the phenotypic space
of human cells has often been viewed as an insurmountable challenge. However, in the last …

SARS-CoV-2 Receptor Angiotensin I-Converting Enzyme Type 2 (ACE2) Is Expressed in Human Pancreatic β-Cells and in the Human Pancreas Microvasculature

D Fignani, G Licata, N Brusco, L Nigi… - Frontiers in …, 2020 - frontiersin.org
Increasing evidence demonstrated that the expression of Angiotensin I-Converting Enzyme
type 2 (ACE2) is a necessary step for SARS-CoV-2 infection permissiveness. In light of the …

Deep learning in image-based phenotypic drug discovery

D Krentzel, SL Shorte, C Zimmer - Trends in Cell Biology, 2023 - cell.com
Modern drug discovery approaches often use high-content imaging to systematically study
the effect on cells of large libraries of chemical compounds. By automatically screening …