From pixels to phenotypes: Integrating image-based profiling with cell health data as BioMorph features improves interpretability

S Seal, J Carreras-Puigvert, S Singh… - Molecular Biology of …, 2024 - Am Soc Cell Biol
Cell Painting assays generate morphological profiles that are versatile descriptors of
biological systems and have been used to predict in vitro and in vivo drug effects. However …

[HTML][HTML] A Decade in a Systematic Review: The Evolution and Impact of Cell Painting

S Seal, MA Trapotsi, O Spjuth, S Singh… - ArXiv, 2024 - ncbi.nlm.nih.gov
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 of …

Artificial intelligence unifies knowledge and actions in drug repositioning

Z Yin, STC Wong - Emerging topics in life sciences, 2021 - portlandpress.com
Drug repositioning aims to reuse existing drugs, shelved drugs, or drug candidates that
failed clinical trials for other medical indications. Its attraction is sprung from the reduction in …

Self-supervised representation learning for high-content screening

D Siegismund, M Wieser, S Heyse… - … on Medical Imaging …, 2022 - proceedings.mlr.press
Biopharma drug discovery requires a set of approaches to find, produce, and test the safety
of drugs for clinical application. A crucial part involves image-based screening of cell culture …

Learning Channel Importance for High Content Imaging with Interpretable Deep Input Channel Mixing

D Siegismund, M Wieser, S Heyse… - DAGM German Conference …, 2023 - Springer
Uncovering novel drug candidates for treating complex diseases remain one of the most
challenging tasks in early discovery research. To tackle this challenge, biopharma research …

VONet: A deep learning network for 3D reconstruction of organoid structures with a minimal number of confocal images

E Song, M Kim, S Lee, HW Liu, J Kim, DH Choi… - Patterns, 2024 - cell.com
Organoids and 3D imaging techniques are crucial for studying human tissue structure and
function, but traditional 3D reconstruction methods are expensive and time consuming …

[HTML][HTML] Benchmarking feature selection methods for compressing image information in high-content screening

D Siegismund, M Fassler, S Heyse, S Steigele - SLAS technology, 2022 - Elsevier
Biopharmaceutical drug discovery, as of today is a highly automated, high throughput
endeavor, where many screening technologies produce a high-dimensional measurement …

PCIM: Learning Pixel Attributions via Pixel-wise Channel Isolation Mixing in High Content Imaging

D Siegismund, M Wieser, S Heyse… - arXiv preprint arXiv …, 2024 - arxiv.org
Deep Neural Networks (DNNs) have shown remarkable success in various computer vision
tasks. However, their black-box nature often leads to difficulty in interpreting their decisions …

High Content Analysis Across Signaling Modulation Treatments for Subcellular Target Identification Reveals Heterogeneity in Cellular Response

S Biswas - Frontiers in Cell and Developmental Biology, 2021 - frontiersin.org
Cellular phenotypes on bioactive compound treatment are a result of the downstream
targets of the respective treatment. Here, a computational approach is taken for downstream …

Using Cell Painting and Chemical Data for Small-molecule Bioactivity and Toxicity Prediction

S Seal - 2024 - repository.cam.ac.uk
High-content image-based assays have fueled significant discoveries in the life sciences in
the past decade, including novel insights into disease etiology, mechanism of action, new …