Seminar series on applied bioimage analysis

The Center for Computational Biomedicine (CCB) is hosting a joint seminar series with the Image Analysis Collaboratory (IAC) at Harvard Medical School with a focus on best practices and leading tools for quantitative analysis of biomedical images.

Using high content analysis and deep learning to make the most of your microscopy

• Date: Monday, December 11th, 2023
• Time: 10:00 - 11:00 AM EDT
• Speaker: Beth Cimini, PhD. Broad Institute, Boston, MA.
• Topic: Using high content analysis and deep learning to make the most of your microscopy
• Location: Gordon Hall 106 Waterhouse Conference Room
  • Coffee and cookies available on site
• Virtual: Zoom link
  • Coffee and cookies is your own responsibility
• Abstract: In the age of the digital camera, microscopy images constitute a fantastically rich source of quantiative data. Yet, it currently remains difficult for most scientists to mine quantitative data from these images easily such that they can answer their important biological questions. In this talk, we will discuss open source tools that make quantitative image analysis both easier and more reproducible, as well as bioinformatic approaches allowing users to extract novel connections from their data.
• Bio: Dr. Beth Cimini is the Associate Director for Bioimage Analysis and a CZI Imaging Scientist in the Imaging Platform at the Broad Institute in Cambridge, MA.  She obtained a PhD in Biochemistry and Molecular Biology with Dr. Elizabeth Blackburn at UCSF, studying splicing variants of the telomere master scaffolding protein TIN2.  This work honed her interests in image analysis, leading her to postdoctoral and staff scientist roles with Dr. Anne Carpenter’s lab at the Broad, leading a team collaborating with ~30 outside scientists per year on custom image analysis projects.  The Cimini lab focuses on bioimage analysis tool creation (Piximi) and maintenance (CellProfiler), as well as on applying open source tools to novel biological problems.  She created and directs the Platform’s Postdoctoral Training Program in Bioimage Analysis, and also leads the Broad efforts on community engagement and technology development for the Center for Open Bioimage Analysis (COBA).
• See also: https://cimini-lab.broadinstitute.org

glue genes: Exploratory Data Analysis for Single Cell and Spatial Omics

• Date: Monday, June 26th, 2023
• Time: 10:00 - 11:00 AM EDT
• Speaker: Jonathan Foster, PhD. glue solutions, Inc.
• Topic: glue genes: Exploratory Data Analysis for Single Cell and Spatial Omics 
• Location: Countway Library 5th floor, Lahey Room 518
  • Coffee and cookies available on site
• Virtual: Zoom link
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• Abstract: glue genes is a new open source tool bringing the power of the glue visualization library to analysis of single-cell and spatial omics data. The core features of glue genes are (1) flexible linking of diverse, multi-dimensional datasets, (2) automatic connections across multiple visualizations, and (3) easy extensibility and integration with other open source Python tools. I will talk about the philosophy and design of glue genes, and show examples of how it can be used to explore linked datasets in real time, showcasing the desktop application as well as the in-development “glupyter” project, which puts the power of glue inside Jupyter Lab. glue genes is developed in partnership with the Jackson Laboratory.
• Bio: Jonathan Foster is Chief Technical Officer of glue solutions, Inc. After earning his Ph.D. in astronomy at Harvard, he worked as a director of data science in the movie industry. Seeing deficiencies in the tools available for exploratory data analysis, he joined glue solutions in 2021. He is not a biologist, but has been working with them long enough to have picked up some of the jargon.
• See also: https://glueviz.org/

Napari: A multi-dimensional data viewer for Python

• Date: Monday, May 1, 2023
• Time: 3:00 – 4:00 PM EDT
• Speaker: Talley Lambert, PhD, Associate Director of Imaging Technology @ Nikon Imaging Center, Harvard Medical School; Core Developer, Napari
• Topic: Napari: A multi-dimensional data viewer for Python
• Location: Countway Library 5th floor, Lahey Room 518
  • Coffee and cookies available on site
• Virtual: Zoom link
  • Coffee and cookies is your own responsibility
• Abstract: With the advent of new multiplexed tissue imaging technologies, there is a growing need for efficient tools for browsing, annotating, and analyzing large multi-dimensional images. In this seminar, Talley will discuss Napari, an open source, interactive, multi-dimensional data viewer for Python.