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PSLID - VCell Integration

Collaborative project between CMU and UCHC

Overview

The goals of this project are:

  • to make several resources developed and maintained at CMU available to VCell users
  • to develop standards for generative model encodings that facilitate use by modeling and simulation tools

The PDF file of the project description from the original supplement application is available for reference (in the list of attachments at the bottom, and also with a direct link here: continuation-proj2.pdf)

The list of major features/functionalities to be added to VCell:

  • import real microscopy image data from PSLID database to:
    • create VCell geometries (compartment boundaries)
    • create VCell field data (protein distributions)
  • use trained generative models from PSLID database to:
    • create "virtual" cell geometries
    • create "virtual" protein distributions
    • add "virtual" protein data to "real" cell geometries and protein data

Aim 1: PSLID interface for VCell

VCell prototype application for selecting and uploading segmented images into geometries is functional.

Outstanding issues with PSLID (after March 12 videoconference): (please update with details and change No to DONE as appropriate)

Outstanding issues with PSLID (for the new version 4 of PSLID): (please update with details and change No to DONE as appropriate)

Outstanding issues with VCell protoype UI for PSLID: (please update with details and change No to DONE as appropriate)

  • VCell Geometry SaveAs... fails with JDOM IllegalDataException (3/17/08)
    • fixed DONE, tested DONE - Frank (temp fix, pslid branch version 2230)
  • PSLID available data queries lump experimental and generated imaged in pulldown combobox (3/17/08)
    • fixed DONE - Dan 3/17
    • tested DONE - Ion 3/17
  • UPDATEDPSLID Browser dialog box preferred size needs to be set at 550x600 (3/20/08)
    • fixed DONE (Dan), tested DONE (Dan 3/20/08)
  • Experimental image download only keeps some of the metadata (sizes, etc.) - the rest (microscope info etc.) should not be discarded, but saved as field data annotation (3/17/08)
    • UPDATEDfixed DONE (Dan), tested DONE (Dan 3/20/08) we display protocol and microscope information in the annotation field
  • Query Strings for URLs are not checked/protected (e.g spaces must be replaced with %20 etc.)
    • fixed No, tested No

Aim 2: Virtual geometries

VCell prototype application for importing generated images is (almost) functional.

  • It currently supports this format: 2 color outlines (cell, nucleus) + 1 color halftone data (protein)
  • It currently splits data into 2 objects to be saved: one 2D geometry and one field data

Outstanding issues with PSLID (after March 12 videoconference): (please update with details and change No to DONE as appropriate)

Aim 3: SBML-compatible standard for generative models

Work has not yet started.

Presentations

Info on posters and talks related to this collaboration

TCNP All-Hands (March 20-21, 2008)

Here's a link to the Agenda of the meeting.

Outline of the presentation:

  1. (Bob) Overview of PSLID/SLIF + why it can be useful to VCell users
  2. (Ion) Overview of VCell + how it can be consumer to PSLID/SLIF
  3. (Bob) New resources and other developments in PSLID to support VCell
  4. (Ion) New interface and other developments in VCell to connect to PSLID + live demo (maybe...)

Topic attachments
I Attachment Action Size Date Who Comment
PowerPointppt 20080321_TCNP_part1_v03.ppt manage 7288.5 K 2008-03-21 - 03:02 BobMurphy Part 1 of talk
PowerPointppt 20080321_TCNP_part2_v02.ppt manage 1014.0 K 2008-03-21 - 03:05 BobMurphy Bob second part
PowerPointppt VCell_TCNP_PSLID.ppt manage 389.0 K 2008-03-21 - 15:29 IonMoraru Ion second part
PowerPointppt VCell_TCNP_overview.ppt manage 8884.0 K 2008-03-21 - 15:28 IonMoraru Ion overview
PDFpdf continuation-proj2.pdf manage 27.1 K 2008-03-13 - 20:54 IonMoraru Project description in the original supplement application
JPEGjpg pslid_voids.jpg manage 166.1 K 2008-03-20 - 22:08 FrankMorgan Demonstration of malformed cell body compartment
Topic revision: r26 - 2008-09-26 - 18:01:07 - DanVasilescu
 
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