204 citations · 672 across the 14 of their papers we have counts for
14 papers
GloBIAS: strengthening the foundations of BioImage Analysis
Agustin Andres Corbat, Christa G Walther, Laura Rodríguez de la Ballina +14
There is a global need for BioImage Analysis (BIA) as advances in life sciences increasingly rely on cutting-edge imaging systems that have dramatically expanded the complexity and…
Evaluating Integrative Strategies for Incorporating Phenotypic Features in Spatial Transcriptomics
Levin M Moser, Ahmad Kamal Hamid, Esteban Miglietta +2
Spatial transcriptomics (ST) technologies not only offer an unprecedented opportunity to interrogate intact biological samples in a spatially informed manner, but also set the stag…
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…
Creating and troubleshooting microscopy analysis workflows: common challenges and common solutions
Beth A Cimini
As microscopy diversifies and becomes ever-more complex, the problem of quantification of microscopy images has emerged as a major roadblock for many researchers. All researchers m…
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…
Defining the boundaries: challenges and advances in identifying cells in microscopy images
Nodar Gogoberidze, Beth A. Cimini
Segmentation, or the outlining of objects within images, is a critical step in the measurement and analysis of cells within microscopy images. While improvements continue to be mad…
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…
The Multi-modality Cell Segmentation Challenge: Towards Universal Solutions
Jun Ma, Ronald Xie, Shamini Ayyadhury +37
Cell segmentation is a critical step for quantitative single-cell analysis in microscopy images. Existing cell segmentation methods are often tailored to specific modalities or req…
Pseudo-Labeling Enhanced by Privileged Information and Its Application to In Situ Sequencing Images
Marzieh Haghighi, Mario C. Cruz, Erin Weisbart +9
Various strategies for label-scarce object detection have been explored by the computer vision research community. These strategies mainly rely on assumptions that are specific to…
CellProfiler plugins -- an easy image analysis platform integration for containers and Python tools
Erin Weisbart, Callum Tromans-Coia, Barbara Diaz-Rohrer +7
CellProfiler is a widely used software for creating reproducible, reusable image analysis workflows without needing to code. In addition to the >90 modules that make up the main Ce…
Roadmap on Deep Learning for Microscopy
Giovanni Volpe, Carolina Wählby, Lei Tian +72
Through digital imaging, microscopy has evolved from primarily being a means for visual observation of life at the micro- and nano-scale, to a quantitative tool with ever-increasin…
Understanding metric-related pitfalls in image analysis validation
Annika Reinke, Minu D. Tizabi, Michael Baumgartner +75
Validation metrics are key for the reliable tracking of scientific progress and for bridging the current chasm between artificial intelligence (AI) research and its translation int…
Distributed-Something: scripts to leverage AWS storage and computing for distributed workflows at scale
Erin Weisbart, Beth A. Cimini
Distributed-Something coordinates the distribution of any Dockerized workflow using on-demand computational infrastructure from Amazon Web Services to enable at-scale workflows whe…
CellProfiler Analyst 3.0: Accessible data exploration and machine learning for image analysis
David R. Stirling, Anne E. Carpenter, Beth A. Cimini
Image-based experiments can yield many thousands of individual measurements describing each object of interest, such as cells in microscopy screens. CellProfiler Analyst is a free,…