Constructing a Common Coordinate Framework for the Human Lung


Where: Harvard Medical School
When: Thursday, June 27, 2019 8:30 AM to 3:00 PM EST
Registration: Please register in advance here, to participate via WebEx


The Human Biomolecular Atlas Program (HuBMAP) aims to catalyze development of a framework for mapping of the human body at high resolution, and to generate foundational 3D tissue maps that integrate high-content, high-throughput imaging and 'omics assays. The construction of a Common Coordinate Framework (CCF) represents a key component of this effort, in order to reproducibly define any location in the human body, and to enable consistent spatial referencing across individuals. This workshop is organized by one of the two HuBMAP Mapping Centers (led by Rahul Satija, John Marioni, and Aviv Regev). We have chosen to focus this workshop on a potential pilot project in the human lung, both because there has been extensive prior work in this area, but also because there are multiple communities (including the NIH LungMAP project, and the Human Cell Atlas Lung Consortium), all of whom have deep interest and expertise in this area and may benefit from joint discussion.

Specific topics to be addressed:

  • How can we optimally define a sampling strategy to spatially register samples?
  • How can we compare lungs across the dynamic, physiological, breathing process?
  • What physiological 'landmarks' can be used to construct a CCF?
  • What is the extent of their anatomical conservation across individuals?
  • What tools are needed to create a coherent, consistent, and integrated set of cell types/states in the lung?
  • How will the broader community use the lung CCF?

Due to limited seating, in-person attendance is by invitation. However, all talks will be recorded via WebEx and available for livestreaming, and virtual participation is open to the community. If you would like to register to participate virtually, please sign up here.


8:30 am — 8:40 am Organizers and NIH
Welcome and Introduction
8:40 am — 9:10 am Tushar Desai Stanford University
Spatial Architecture and Organization of the Human Lung
9:10 am — 9:40 am Gloria Pryhuber University of Rochester
Lung: Old and new. Procurement, Processing, and Analysis for LungMAP and HuBMAP
9:40 am — 9:55 am Kun Zhang UCSD
Creating a Lung Airways and Prenchymal Map (LAPMAP)
9:55 am — 10:10 am Katy Borner University of Indiana
User interfaces and registration pipelines for the HuBMAP CCF
10:10 am — 10:30 am Alexander Misharin Northwestern University
The Human Lung Cell Atlas Seed Network
10:30 am — 10:45 am Coffee Break
10:45 am — 11:00 am Rahul Satija New York Genome Center
Introduction to creating a Lung CCF: Strategies and Challenges
11:00 am — 11:30 am Joseph Reinhardt University of Iowa
Segmentation, analysis, and registration of the human airway tree from 3D X-ray CT images
11:30 am — 12:00 pm Graham Barr Columbia University
Variation in lung structure in the general population
12:00 pm — 1:15 pm Lunch and Discussion
1:15 pm — 1:45 pm Jay Rajagopal Massachussets General Hospital
The Airway Epithelial Ensemble
1:45 pm — 2:15 pm Martijn Nawijn Massachussets General Hospital
A cellular census of human lungs identifies novel cell states in health and in asthma
2:15 pm — 3:00 pm Discussion


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