**This workshop has ended. View the recording here.**

Workshop 4: Connectome generation and data pipelines

MARCH 17, 2021

Goal: To identify the current state of the art, challenges and opportunities associated with connectome generation and data pipelines.

Draft Agenda: [Click here to download PDF version]

11:00 am ET

Welcome and Series Overview
John Ngai and Harriet Kung

11:10 am ET

Welcome and Introduction
Workshop co-leads: Nicola Ferrier and Viren Jain

11:20 am ET

Workshop Logistics

11:25 am ET


Each speaker will address three questions:

  1. What are the prospects and challenges you see in scaling your approach (and/or analysis goals in general) to volumes comprising hundreds of petavoxels of imaging data?
  2. What kinds of general improvements in technical infrastructure (hardware and/or software) would mostly dramatically aid in scaling your analysis?
  3. What new frontiers of analysis (especially as may be enabled by, or complementary to, a whole mammalian connectome) are you most excited by? What challenges do you see in pursuing those frontiers?

11:25 am ET

Speaker Session 1 – Volume assembly (stitching, alignment, registration)

11:25 pm ET

Volume Assembly in the context of a large scale Connectomics pipeline
Gayathri Mahalingam

11:35 pm ET

Scalable stitching and alignment for 3D electron microscopy
Stephan Saalfeld

11:45 pm ET

Alignment of serial section EM for automated reconstruction
Thomas Macrina

11:55 am ET


12:05 pm ET

Speaker Session 2 – Automated reconstruction and annotation (segmentation,
synapses, types, compartments)

12:05 pm ET

Automated dense reconstruction of neural tissue
Michal Januszewski

12:15 pm ET

Synapse Detection in a Fly Brain
Julia Buhmann

12:25 pm ET

Towards a parts list for a whole mouse brain
Nicholas Turner

12:35 pm ET


12:45 pm ET

Speaker Session 3 – Connectome proofreading, verification, crowd-sourcing

12:45 pm ET

Proofreading the Drosophila Hemibrain Connectome
Patricia Rivlin

12:55 pm ET

Connectome querying and verification
Joergen Kornfeld

1:05 pm ET

Crowdsourcing Connectomics at Scale
Amy Sterling

1:15 pm ET


1:25 pm ET

Speaker Session 4 – HPC, data infrastructure, visualization

1:25 pm ET

Research Data Management at Scale
Rachana Anathakrishnan

1:35 pm ET

Connectomics at ALCF
Tom Uram

1:45 pm ET

Scaling Pipelines for EM Connectomics
Eric Perlman

1:55 pm ET

Q&A session

2:40 pm ET


3:00 pm ET

Discussion Panel

Panel Discussion topic: Reflections on how experience as a computer scientist might inform an ‘exascale’ project aimed at generating comprehensive maps of brain connectivity

Panel Chairs: Nicola Ferrier, Viren Jain

Discussants: Frances Chance, Adrienne Fairhall, Ian Foster, Eugene Myers, Olga Ovchinnikova, Andreas Tolias

4:00 pm ET

Closing remarks / End of workshop
Workshop co-leads: Nicola Ferrier and Viren Jain