Planteome Image Annotation Working Group

Goals and Objectives:

Image_Annotation_Software_Specification

Participants

• Jaiswal Lab (OSU, BPP): Justin Preece, Justin Elser
• Todorovic Group (OSU, EECS): Sinisa Todorovic, Xu Xu, Ryan Kitchen (Yao Zhou has left the project)
• iPlant-Bisque Group (UCSB): Kris Kvilekval, Dmitri Federov, B.S. Manjunath

Image Annotation Working Group Meetings:

Initial Project Meeting: Jan 23, 2015

(Conf. call arranged and hosted on Zoom by Martha Narro, iPlant)

Attendees

• Jaiswal Lab (OSU, BPP): Pankaj Jaiswal, Justin Preece
• Todorovic Group (OSU, EECS): Sinisa Todorovic, Yao Zhou
• iPlant-Bisque Group (UCSB): Kris Kvilekval, Dmitri Federov, B.S. Manjunath

Agenda

• (Re-)Introductions
• Planteome AISO/Bisque proposal review
• Discussion of broad project objectives
• Scheduled next meeting (will be a technical meeting)

Action Items

• Justin send Yao the AISO documentation
• Kris and Dmitry send Yao (and all) pointers to Bisque documentation and Google group.
• Yao: begin to get familiar with Bisque and the AISO Java codebase.

AISO Demo (OSU Only): Tue, Jan 27, 1 PT

Attendees

• Jaiswal Lab (OSU, BPP): Justin Preece
• Todorovic Group (OSU, EECS): Sinisa Todorovic, Yao Zhou, Xu Xu

Agenda

• Demos and technical introductions to AISO and codebase
• Preliminary list of features desired to port to Bisque

Tech Demo Meeting: Thu, Jan 29, noon PT/1p MT

(Conf. call arranged and hosted on Zoom by Martha Narro, iPlant)

Attendees

• Jaiswal Lab (OSU, BPP): Pankaj Jaiswal, Justin Preece
• Todorovic Group (OSU, EECS): Sinisa Todorovic, Yao Zhou, Xu Xu
• iPlant-Bisque Group (UCSB): Kris Kvilekval, Dmitri Federov

Agenda

• Demos and technical introductions to Bisque development environment and AISO functionality
  • Second grad student developer (Xu Xu) added from Sinisa's group
• Discuss IGC segmentation algorithm
• Discuss implementation of a Bisque ontology service
• Project planning and timelines
• Discussed possible attendance at May 14-15 Bisque developer workshop at U of Arizona

Tech Dev Meeting: Tue, Feb 10, 1p PT

Attendees

• Jaiswal Lab (OSU, BPP): Justin Preece
• Todorovic Group (OSU, EECS): Yao Zhou, Xu Xu

Agenda

• Discussed approaches to functionality ahead of Bisque tech mtg
  • Latency in Bisque's current round-trip approach to Graph Cuts segmentations - is it the round-trip or the graph cuts that takes so long? (JP thinks it's the round trip)
  • IGC segmentation algorithm - DCU and Bisque implementations different? (don't know yet)
  • Discuss implementation of segmentation module: general use-case
    • how to capture and transmit user input (foreground/background markup)
    • how to return segmentation results
    • emphasized importance of lean data communication, layered segments, overlap capabilities, undo/redo, how to store points sets and annotation data (in generic data structure terms)
• Project planning and timelines: define an iterative dev approach (multiple phases, with modest & clear initial goals)
  • will flesh out in mtg w/ Bisque team

Bisque Dev Env Setup Meeting: Thu, Feb 12, 1p MT

(Skype call)

Attendees

• Jaiswal Lab (OSU, BPP): Justin Preece, Justin Elser
• Todorovic Group (OSU, EECS): Yao Zhou, Xu Xu
• iPlant-Bisque Group (UCSB): Kris Kvilekval, Dmitri Federov

Agenda

• Sort out issues in setting up Dev environment for YZ, XX
• Tour of Bisque module XML templates and sample MatLab image annotation script
• Define technical approach and requirements for the first phase of software development.
  • Discuss appropriate graph cuts algorithm (will probably use an implementation of Kolmogorov graph cuts
  • Discuss latency in Bisque's current round-trip approach to Graph Cuts segmentations

Action Items

• JP - draft requirements documentation for both the initial round of development, as well as more general objectives for the rest of the Planteome Image Annotation efforts
• All - review, discuss, and bicker over said requirements documentation.  :)
• YZ, XX, DF, KK - Troubleshoot dev environment setup for YZ and XX.
• Next mtg: TBD

PIA Phase 1 Specification Meeting: Fri, Mar 13, 2p PT

(Planteome Zoom call)

Attendees

• Jaiswal Lab (OSU, BPP): Justin Preece
• Todorovic Group (OSU, EECS): Yao Zhou, Xu Xu
• iPlant-Bisque Group (UCSB): Kris Kvilekval

Agenda

• Revise specs for the first phase of software development
• Continue Dev environment setup with YZ, XX

Action Items

• JP - schedule next meeting for late next week (objectives: put timelines on Phase 1, discuss Phase 2/3 goals)
• KK - complete slimmed-down Bisque dev env deployment package for local installs
• All - think about rough timelines for Phase 1 activities
• YZ, XX, DF, KK - Cont. troubleshooting dev environment setup for YZ and XX.
• Next mtg: TBA (3/20?)

PIA Phase 1 Timeline Meeting: Thu, Apr 23, 10a PT

(Cord 3084)

Attendees

• Jaiswal Lab (OSU, BPP): Justin Preece
• Todorovic Group (OSU, EECS): Sinisa Todorovic, Xu Xu, Ryan Kitchen

Agenda

• Discuss personnel changes: Yao Zhou is leaving the project. Ryan Kitchen (undergrad CS) is joining.
• Discuss timeline for Phase 1
• ST raised the issue of being able to run multiple visual analysis steps in a multi-step "pipeline" within this proposed module. Taken under advisement for future phases; and will factor into the initial architecture as much as possible.

Action Items

• JP - schedule official bi-weekly standing PIA developer meeting
• KK - complete slimmed-down Bisque dev env deployment package for local installs
• Next mtg: TBA

PIA Working Group Bi-Weekly Conf Call: Thu, Apr 30, 2p PT

(Cord 3084)

Attendees

• Jaiswal Lab (OSU, BPP): Justin Preece
• Todorovic Group (OSU, EECS): Xu Xu, Ryan Kitchen
• UCSB / Bisque Group: Kris Kvilekval

Agenda

Action Items

PIA Prez Prep Mtg: Tue, May 5, 11:30a PT

(Cord 3084)

Attendees

• Jaiswal Lab (OSU, BPP): Justin Preece
• Todorovic Group (OSU, EECS): Xu Xu, Ryan Kitchen

Agenda

• Prep for UCSB Big Data + Bio-Image Workshop

Action Items

Conferences and Workshops

Big Data + Bio-imaging Workshop: May 14-15, UC-Santa Barbara

Attendees

• Jaiswal Lab (OSU, BPP): Justin Preece
• Todorovic Group (OSU, EECS): Xu Xu

Agenda

Action Items