47 citations · 104 across the 10 of their papers we have counts for
10 papers
JUMP-lite: Compact, reproducible benchmarking of cell representations
Alán F. Muñoz, Johan Fredin Haslum, Runxi Shen +2
Image-based profiling captures rich phenotypic signatures for drug discovery and functional genomics. Large public datasets like JUMP Cell Painting now provide millions of images f…
cubic: CUDA-accelerated 3D Bioimage Computing
Alexandr A. Kalinin, Anne E. Carpenter, Shantanu Singh +1
Quantitative analysis of multidimensional biological images is useful for understanding complex cellular phenotypes and accelerating advances in biomedical research. As modern micr…
Progress and new challenges in image-based profiling
Erik Serrano, John Peters, Jesko Wagner +19
For over two decades, image-based profiling has revolutionized cell phenotype analysis. Image-based profiling processes rich, high-throughput, microscopy data into thousands of unb…
Foreground-aware Virtual Staining for Accurate 3D Cell Morphological Profiling
Alexandr A. Kalinin, Paula Llanos, Theresa Maria Sommer +11
Microscopy enables direct observation of cellular morphology in 3D, with transmitted-light methods offering low-cost, minimally invasive imaging and fluorescence microscopy providi…
cp_measure: API-first feature extraction for image-based profiling workflows
Alán F. Muñoz, Tim Treis, Alexandr A. Kalinin +4
Biological image analysis has traditionally focused on measuring specific visual properties of interest for cells or other entities. A complementary paradigm gaining increasing tra…
Learning Molecular Representation in a Cell
Gang Liu, Srijit Seal, John Arevalo +4
Predicting drug efficacy and safety in vivo requires information on biological responses (e.g., cell morphology and gene expression) to small molecule perturbations. However, curre…
MOTIVE: A Drug-Target Interaction Graph For Inductive Link Prediction
John Arevalo, Ellen Su, Anne E Carpenter +1
Drug-target interaction (DTI) prediction is crucial for identifying new therapeutics and detecting mechanisms of action. While structure-based methods accurately model physical int…
A Decade in a Systematic Review: The Evolution and Impact of Cell Painting
Srijit Seal, Maria-Anna Trapotsi, Ola Spjuth +5
High-content image-based assays have fueled significant discoveries in the life sciences in the past decade (2013-2023), including novel insights into disease etiology, mechanism o…
Cell Painting Gallery: an open resource for image-based profiling
Erin Weisbart, Ankur Kumar, John Arevalo +3
Image-based or morphological profiling is a rapidly expanding field wherein cells are "profiled" by extracting hundreds to thousands of unbiased, quantitative features from images…
Reproducible image-based profiling with Pycytominer
Erik Serrano, Srinivas Niranj Chandrasekaran, Dave Bunten +25
Advances in high-throughput microscopy have enabled the rapid acquisition of large numbers of high-content microscopy images. Whether by deep learning or classical algorithms, imag…