Robust nucleus/cell detection and segmentation in digital pathology and microscopy images: a comprehensive review

F **ng, L Yang - IEEE reviews in biomedical engineering, 2016‏ - ieeexplore.ieee.org
Digital pathology and microscopy image analysis is widely used for comprehensive studies
of cell morphology or tissue structure. Manual assessment is labor intensive and prone to …

[HTML][HTML] Machine learning and image-based profiling in drug discovery

C Scheeder, F Heigwer, M Boutros - Current opinion in systems biology, 2018‏ - Elsevier
The increase in imaging throughput, new analytical frameworks and high-performance
computational resources open new avenues for data-rich phenotypic profiling of small …

Cellpose3: one-click image restoration for improved cellular segmentation

C Stringer, M Pachitariu - Nature Methods, 2025‏ - nature.com
Generalist methods for cellular segmentation have good out-of-the-box performance on a
variety of image types; however, existing methods struggle for images that are degraded by …

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 …

Learning representations for image-based profiling of perturbations

N Moshkov, M Bornholdt, S Benoit, M Smith… - Nature …, 2024‏ - nature.com
Measuring the phenotypic effect of treatments on cells through imaging assays is an efficient
and powerful way of studying cell biology, and requires computational methods for …

An automatic learning-based framework for robust nucleus segmentation

F **ng, Y **e, L Yang - IEEE transactions on medical imaging, 2015‏ - ieeexplore.ieee.org
Computer-aided image analysis of histopathology specimens could potentially provide
support for early detection and improved characterization of diseases such as brain tumor …

CellProfiler: image analysis software for identifying and quantifying cell phenotypes

AE Carpenter, TR Jones, MR Lamprecht, C Clarke… - Genome biology, 2006‏ - Springer
Biologists can now prepare and image thousands of samples per day using automation,
enabling chemical screens and functional genomics (for example, using RNA interference) …

Accurate information transmission through dynamic biochemical signaling networks

J Selimkhanov, B Taylor, J Yao, A Pilko, J Albeck… - Science, 2014‏ - science.org
Stochasticity inherent to biochemical reactions (intrinsic noise) and variability in cellular
states (extrinsic noise) degrade information transmitted through signaling networks. We …

EBImage—an R package for image processing with applications to cellular phenotypes

G Pau, F Fuchs, O Sklyar, M Boutros, W Huber - Bioinformatics, 2010‏ - academic.oup.com
EBImage provides general purpose functionality for reading, writing, processing and
analysis of images. Furthermore, in the context of microscopy-based cellular assays …

CellProfiler™: free, versatile software for automated biological image analysis

MR Lamprecht, DM Sabatini, AE Carpenter - Biotechniques, 2007‏ - Taylor & Francis
Careful visual examination of biological samples is quite powerful, but many visual analysis
tasks done in the laboratory are repetitive, tedious, and subjective. Here we describe the use …