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 to as appropriate)

• image missing/empty on page returned by specific query
  • fixed
  • tested by Dan (03/14/08)
    query: http://pslid.cbi.cmu.edu/develop/makecompartmentimage.jsp?regionid=523&stackpos=1
• segmented image has protein distro filled with same pixel value instead of scaled values
  • fixed - protein values and cell regions provided as separate downloadable images (scaled and color-mapped, respectively)
  • tested
• image data returned is JPEG, not TIFF
  • fixed
  • tested by Dan (03/14/08), duration 30 sec
    query: http://pslid.cbi.cmu.edu/develop/makecompartmentimage.jsp?regionid=523&stackpos=1
• 2 specific queries take way too long (minutes)
  • one type is images by protein target
    example query: http://pslid.cbi.cmu.edu/develop/searchreturnxml.jsp?target=giantin (usually > 5 mins)
  • kludge for demo purposes (Jenn 3/17) - use temp database (http://pslid.cbi.cmu.edu/tcnp/...) that only has one dataset (2D HeLa)
    example query: http://pslid.cbi.cmu.edu/tcnp/searchreturnxml.jsp?target=giantin (< 5 sec)
  • partially fixed ; (Dan): the above query works but image recovery query returns HTTP error 500
    for example: http://pslid.cbi.cmu.edu/tcnp/makecompartmentimage.jsp?regionid=523&stackpos=1
    (Jenn 3/19): makecompartmentimage.jsp debugged
    fixed (Jenn), tested (Dan 3/20/08)
• PSLID "Experimental" data (e.g. HeLa/giantin id=527) sometimes has malformed "cell body" compartment (3/17/08)
  • - did anybody reproduce this error?? Yes, See attachment pslid_void.jpg. fixed , tested
• PSLID "generated" data needs to provide "pixel size" information (3/17/08)
  • fixed , tested

Outstanding issues with PSLID (for the new version 4 of PSLID): (please update with details and change to as appropriate)

• Unable to retrieve segmented images for some image sets
  • fixed
    for example the pair HeLa, f-Actin, image set 1355
    query: http://pslid.cbi.cmu.edu/public4/makecompartmentimage.jsp?regionid=1355&stackpos=1
• Java Virtual Machine running out of memory
  • fixed
    The results list is really huge, IE itself hangs for 1-2 minutes
    this happens for the pair HeLa, DNA - when trying to retrieve the list of images
    query: http://pslid.cbi.cmu.edu/public4/searchreturnxml.jsp?target=DNA&cell_name=HeLa

Outstanding issues with VCell protoype UI for PSLID: (please update with details and change to as appropriate)

• VCell Geometry SaveAs... fails with JDOM IllegalDataException (3/17/08)
  • fixed , tested - Frank (temp fix, pslid branch version 2230)
• PSLID available data queries lump experimental and generated imaged in pulldown combobox (3/17/08)
  • fixed - Dan 3/17
  • tested - Ion 3/17
• PSLID Browser dialog box preferred size needs to be set at 550x600 (3/20/08)
  • fixed (Dan), tested (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)
  • fixed (Dan), tested (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 , tested

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 to as appropriate)

• password login required for generative model queries
  • fixed ,
  • tested - by Dan (03/13/08) - it's very slow (5 minutes)
• no query exists to return list of available trained generative models
  • fixed
    query is: http://pslid.cbi.cmu.edu/develop/return_xml_list.jsp?listtype=gen_model
  • tested - by Ion (03/16/08) - works fast

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...)