The CytoData2023 Symposium includes educative workshops during the first day of the event. The workshops are hosted by Recursion, Calico, and ThinkCyte.

Biological Cartography: Building and Benchmarking Representations of Life

Purpose: By the end of the workshop, participants should have a good understanding of what maps of biology are, and how to build and benchmark them using image-based profiles.

Presentation: Participants will be introduced to Recursion, its mission, and its approach to industrializing drug discovery. They will learn how Recursion builds and benchmarks maps of biology using image-based profiles (as outlined in this paper co-authored by Recursion and Genentech), and uses these maps for drug discovery. Along the way, participants will gain an understanding of what an EFAAR pipeline is, as well as discuss the issues one should consider when configuring these pipelines for different applications. Existing implementations of EFAAR pipelines will be used as motivating examples. Participants will also be introduced to a suite of metrics that can be used to benchmark and compare different maps of biology.

Demo: Using a publicly-available notebook, participants will follow along as they learn to build and benchmark maps of biology on their own, using embeddings from the public image sets RxRx3 and JUMP-CP. The notebook will use code from the public EFAAR_benchmarking repo.


Unbiased morphological profiling: state-of-the-art applications and emerging frontiers


  • Introduction of Calico
  • Panel discussion. Panelists: Anne Carpenter, Juan Caicedo, Marta Fay, and Leena Latonen
  • Q&A from the audience


  • Definition of morphological profiling: unbiased analysis of cellular/tissue morphology data
  • Advantages of morphological profiling approaches:
    • Unbiased morphological profiles are information rich, at least on par with other omics profiles
    • Morphological phenotypes can reflect cell states comprised of genetic, transcriptomic, proteomic and metabolomic characteristics
    • Morphological phenotypes can be more subtle than what humans can visually perceive
    • Morphological profiling applied to cell culture systems can achieve very high throughput and is cost-efficient on a per-sample basis.

Panel discussion outline

  • Introductions
  • Applications: What are you using unbiased morphological profiling for?
  • Interpretability
  • Emerging frontiers in unbiased biological profiling
  • What do you think are the next big challenges in modeling and analysis (or what do you think are the most exciting current advances)?
  • Quick-fire: What do you think of of the following emerging technologies: a) Pooled optical screening, b) Live cell imaging, c) Organoids and co-culture based morphological screens, d) Spatial profiling (e.g., spatial transcriptomics a la Visium, Xenium, CosMX etc. or spatial proteomics / lipidomics / metabolomics a la MIBI, CODEX, CellDive, Comet etc.)

Ghost Cytometry: An AI-ML technology for High Resolution, Label-free Cellular Fingerprinting

Ghost Cytometry technology is an AI-based hi-res label-free cell analysis and sorting technology for cell therapeutic development and drug discovery providing an entirely new window into Cellular Fingerprinting. In this workshop, we will cover how the technology enables detection of intra-cellular morphological structures and restructuring.  The VisionSort System is the first instrument that allows the physical analysis and sorting of cells based on their morphology, cytoskeletal structure using AI-based technology.  With > 9 million features of high dimensional information per second, VisionSort can profile intracellular structures and spatial information across a wide range of applications.