Image processing, visual analytics, and data sharing for whole-slide imaging and spatial profiling of tissues and tumors

Mar 11, 2024

Jointly hosted with the Center for Computational Biomedicine (CCB)
Seminars are usually made available on YouTube shortly afterwards.

  • Date: Monday, March 11th, 2024
  • Time: 10:00 - 11:00 AM EDT
  • Speaker: Jeremy Muhlich, Director of Software Engineering, Laboratory of Systems Pharmacology, HMS, Boston, MA.
  • Topic: Image processing, visual analytics, and data sharing for whole-slide imaging and spatial profiling of tissues and tumors
  • Location: Gordon Hall 106 Waterhouse Conference Room
    • Coffee and cookies available on site
  • Virtual: Zoom link
    • Coffee and cookies is your own responsibility
  • CCB seminar link
  • Abstract: Spatial ‘omics has emerged as a breakthrough technology for understanding the types and states of cells in the intact environment of tissues and tumors. High-plex immunofluorescence microscopy is particularly effective because it builds on two centuries of histopathology and tissue biology, exploits the latest advances in computational microscopy, and links changes in protein levels to changes in morphology at the subcellular level. This talk will describe the overall approach and specific tools used in the Laboratory of Systems Pharmacology covering the entire lifecycle of high-plex whole-slide imaging: 1) Extract quantitative single-cell data from extremely large whole-slide tissue images via an automated pipeline (MCMICRO); 2) Support visual analytics tools directed by human experts to interpret nuanced tissue features and subcellular morphologies beyond the current capability of computational methods (Minerva Analysis); and 3) Enable effective public release of integrated datasets by presenting images and analysis results together in a novel web-based storytelling interface (Minerva Story).
  • Bio: Jeremy Muhlich, Principal Associate, is the Director of Software Engineering at the Harvard Medical School Laboratory of Systems Pharmacology where he supervises a small team that builds, maintains and teaches computational tools to support the collection, processing, visualization and public release of data in the areas of whole-slide and high-throughput microscopy as well as mathematical modeling of cell signaling networks. He has previously worked at the HMS Institute for Chemistry and Cell Biology and the MIT Department of Biology.