5 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…
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…
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…
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…