Big data+ Biomedical Image Informatics: May 14-15 @ UCSB

UCSB Center for Bio-Image Informatics,  iPlant Collaborative, and the Center for Multimodal Big Data Science and Healthcare



08:15 AM Arrival at West Conference Center

08:30 AM Coffee and informal introduction

Morning Session: BisQue - Experiences

08:50 AM Introductions: Manjunath

09:00 AM Nirav Merchant, U. Arizona. iPlant+BisQue Introduction

09:30 AM Joel Schwartz, Pfizer. BisQue@Pfizer/TissueVision

09:50 AM Edgar Spalding, U. Wisconsin. Measuring phenotypes in populations of plants with image analysis (Information on recent Bioimaging workshop at Madison: Storify, notes)

10:10 AM Coffee Break

10:30 AM Dan Szemanski, Purdue (plant image segmentation)

10:50 AM Evan Daugharthy, Church Lab, Harvard U., FISSEQ project

11:10 AM Nikhil Chacko, Liebling Lab, UCSB. Leveraging BisQue for atlas of developing embryonic heart

11:30 AM – 1 :00 PM Working Lunch (served)

Demo of existing tools and pipelines: Moderators: Dmitry Fedorov and Kristian Kvilekval

  • DIRT: Abhi Das and Alexander Bucksch (GA tech)
  • Phenomics in Agriculture: Stephen Welch and Nan An (KState)
  • 3D reconstruction: Kyle Simek (U. of Arizona)
  •  Justin, Oregon State. AISO > PIA project

Afternoon Sesssion: BisQue developers

1:00 PM Kristian Kvilekval, UCSB. BisQue 05 and BisQue 06 roadmap

1:20 PM Fedorov/Delany: Advanced Visualization and 3D Viewer usage

1:30 PM Christian Lang: Indexing and search across multi-modal documents

2:00 – 5:00 PM

Outline hackathon activities and goals:

  • Refine and prioritize hackathon ideas
  • Outline plan for hacking
  • Commence hacking

4:45 PM Kris/Manjunath/Nirav : closing

5:00 PM End for the day

Friday, May 15th

Arrival at Engineering Sciences Building (ESB), room 2001

Morning Session: Big Data Challenges, Large Scale Image Processing

09:00 AM Sindhu Ghanta, Andy Beck’s lab@Harvard: Big Data Image Informatics for Computational Pathology

09:20 AM Wei-Chung Allen Lee, Harvard: Functional assemblies of pyramidal cells in the visual cortex

10:00 AM Sean Donegan, Dream.3D. Materials Science applications

10:20 AM Dmitry Fedorov/Robert Miller, UCSB: Application to underwater and aerial imagery

10:40 AM Coffee break

10:50 - 11:45 AM Open topic discussion: Attributes of a responsive, innovative cyberinfrastructure
for image analysis (ALL PARTICIPANTS)

  • data centric: Challenges and barriers in managing multimodal data
  • analysis centric: Challenges and barriers in developing methods, analysis routines for image analysis (core libraries, productivity improvement when developing new methods group discussion)
  • platform centric: Challenges and barriers in building imaging platform applications/pipelines for communities (user management, computation infrastructure, sustainability)

11 45 AM – 1:00 PM Working Lunch

Demo of hackathon progress

Moderators: Dmitry Fedorov and Kristian Kvilekval

1:00 PM Wrap up (Kris, Nirav)

2:00 PM Atul Butte: Translating a trillion points of data into therapies, diagnostics, and new insights into disease