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User Story #1970 (closed)

Opened 14 years ago

Closed 11 years ago

FLIM in OMERO

Reported by: dzmacdonald Owned by: jburel
Priority: major Milestone: Unscheduled
Component: Scripting Keywords: FLIM, Collaboration
Cc: jburel, jrswedlow, d.lleres@…, p.schofield@…, geoff@…, jamoore, jos@…, s.hutten@…, A.Visvanathan@… Story Points: n.a.
Sprint: n.a. Importance: Exciter
Total Remaining Time: 0.0d Estimated Remaining Time: n.a.

Description (last modified by jburel)

In collaboration with the BioInformatics group in Dundee we will add FLIM functionality to OMERO.

Current Workflows

Currently users using SPCImage have to go through a number of steps to generate their analysis results.

Here are some more details on the workflow to analyse FLIM FRET data:

  1. Launching data corresponding to an acquisition of " No FRET conditions"
    1. Draw an ROI around region of interest (cell, part of cell (nucleus) , different stage of mitosis...)
    2. Determine background level
    3. Determine if it is necessary to increase binning by looking at the average photon count in the ROI.
  2. Perform analysis in SPCImage by applying a monoexponential decay model and fixing the background value.
    1. From the analysis of a single ROI, k no fret = k2 value is output in Excel.
    2. Repeat this analysis of each ROI of a picture and then for n acquisitions of the " No FRET conditions"
    3. Save intensity image as tiff; save k no FRET map as tiff
  3. Calculate a k no fret= k2 average value from the n k2 values analysed.
  4. Launch data corresponding to an acquisition of " FRET conditions"
    1. Draw an ROI around region of interest (cell, part of cell (nucleus) , different stage of mitosis...)
    2. Determine background level
    3. Determine if it is necessary to increase binning by looking at the average photon count in the ROI.
  5. Perform analysis in SPCImage by applying a biexponential decay model and fixing the background value AND FIXING THE K2 PARAMETER FROM THE ANALYSIS (1-3).
    1. From this analysis of a single ROI, k1=k FRET distribution is saved manually as a .csv to be latter open in Excel and displayed in publication.
    2. In SPCimage, for a single ROI generate E 'fret map which is (1-k1/k2*100) ; each map must have min, max lifetime values range set by hand. Displaying E FRET map by using pseudo color continuous or discrete is set up by hand. Save this E FRET map manually as a tiff file.
    3. Repeat this analysis of each ROI of a picture and then for n acquisitions of the " FRET conditions"
  6. Perform calculations in Excel (normalisation FRET populations, etc..)
  7. Combine results to get averages for different treatments, conditions or for different stage of mitosis or cell cycle.


Typically a user will generate 100 fret images per day, each days acquisiton can take up to 2 days to analyse.

OMERO Workflows

  1. In OMERO the user should be able to draw the ROI in different regions on the image
  2. select the fret, no fret images
  3. Run analysis
    1. Generate the Heatmaps and upload/attach in OMERO
    2. Generate the summary results
  4. Allow the visualisation of the chi value to see how good the fits are.
    1. Allow thresholding on chi value to remove from heatmap


This will save users many hours of copying and pasting from SPCImage to Excel, and then Excel to other graphing software.

Meetings


Meeting 02/11/10: Pieta, David, Donald, Jos, J-M

Presentation of a possible solution, RAPID and OMERO. Discussions about workflow, deployment. List of actions:

  • Use machine controlled by Jos for now, deploy on local cluster in the next phase (hopefully).
  • Donald convert FLIM script. When done, pass it to Pieta.
  • Donald Jos, install OMERO later in the week.
  • J-M, familiarize with XML files for RAPID.
  • J-M, David meeting early next week for visualization discussion.

Meeting 24/11/10: Pieta, David, Donald, J-M, Jason

First demo of RAPID running script provided by Pieta.

  • Upload files
  • Run script
  • Display output in Web browser.

Second Phase RAPID and OMERO will be presented next Tuesday
Various discussions where to deploy it after the demo phase i.e. Dundee, Edinburgh.
Resources allocated for that in terms of machines and manpower.
Actions:

  • Pieta: provide lib for latex
  • OMERO team: convert script to talk to omero
  • OMERO team: implement visualisation tool
  • OMERO team: run test with actual implementation for large number of images.
  • RAPID: modify portlet

Meeting 07/12/10: Pieta, David, Donald, J-M

Demo "FLIM in OMERO". A week later than originally planned due to bad weather.
server address: escience2.inf.ed.ac.uk

Actions:

  • David review what to do with results i.e. display, more stats, interaction with scripts.
  • OMERO team, adjusts attachments name and use keywords.

Meeting 01/02/11: Pieta, Saskia, Ashwat, J-M, Jason (later) ==

  • Introduce to Saskia and Ashwat what has been done so far.
  • OMERO server now in Dundee, Data analysed in Edinburgh
  • Discussions about how to display results and how to interact with script. Improvement required
  • Pieta and J-M to meet with Saskia and Ashwat on 07/02/11 2pm

Change History (21)

comment:1 Changed 14 years ago by dzmacdonald

  • Description modified (diff)

comment:2 Changed 14 years ago by jmoore

Notes from discussion Mar. 11:

FLIM

 - tasks to get done
  -- NDIM model
  -- get ready for scripts in anger
  -- get ready for new camera
  -- encorporating Pieta's script
   --- it's broken (mathematical, mixed variables)
   --- will take work to get it working
   --- basic version is running against OMERO
  -- optimizations for values like SPImage
  -- dealing with ROIs
   --- drawing them, storing them on the server
   --- some version of trunk (matches scripts)
   --- Donald will work on ROIs today
  -- visualization mechanism (heatmaps)
  -- rolling back the fake FLIM
  -- submissions
   --- submitting 200 images to server
   --- not running it on the server (nor in parallel)

 - time scales
  -- tried to talk to him 2 weeks ago (conference)
  -- he's doing it now. (starts today)

 - discuss NDIM Monday
  -- won't be implementing anything right away
  -- Donald: hacking something up
  -- Jean-Marie: if data comes as now, we're fine

 - tickets
  -- roi
   --- difference which rois for measurement and for viz
   --- namespaces

 - mongo
  -- 3 days away from insight writing to mongo
  -- omero pojos ok
  -- was modifying insight gateway
  -- Chris: means changing everything?
  -- ROI is the starting point (drawing)
  -- Jason: don't like the namespace "measurement"/"visualization" is something user needs to understand
   --- from users POV, need "infinite flexibility" of tagging
   --- Jean-Marie: is going to be extremely painful
  -- Chris: starting with a single keyword (before alternative storage)
  -- NB: tags don't have a namespace right now
  -- combo box drop down with the various workflows
  -- #namespace manager

 - preview
  -- john: get another nightshade
  -- get a grid engine
 
 - decisions
  -- move alternative storage out of sprint
  -- donald works on flim
  -- discuss the plan for next mongo
  -- next sprint: what else suffers?

 - end of this iteration
  -- good chance to have roi, flim working
  -- good chance of some visualization
  -- some heatmap, uploaded as an image or jpeg annotation
  -- may not be fast (on cluster)
  -- how much work to get scripting working?

 - iteration 5
  -- by end, flim done? no, but handing something to david by next week
  -- on the cluster (or optimized)
  -- (conservative and add a extra week, i.e. middle of week)

 - docs for clients
  -- Examples of different things in the scripts

 - things that have to be maintained
  -- matlab / cellprofiler

 - shooting for a middle ground
  -- have to decide what we're going for (4.2)
  -- is there any technological middle ground?
  -- 

comment:3 Changed 14 years ago by jburel

  • Description modified (diff)

comment:4 Changed 14 years ago by jburel

  • Description modified (diff)

comment:5 Changed 14 years ago by dzmacdonald

  • Description modified (diff)

comment:6 Changed 14 years ago by dzmacdonald

  • Description modified (diff)

comment:7 Changed 14 years ago by jburel

  • Sprint 2010-03-05 (4) deleted

comment:8 Changed 13 years ago by jburel

  • Cc d.lleres@… p.schofield@… geoff@… jmoore jos@… added
  • Description modified (diff)

comment:9 Changed 13 years ago by jmoore

  • Milestone changed from Unscheduled to OMERO-Beta4.3

comment:10 Changed 13 years ago by jburel

  • Description modified (diff)
  • Priority set to minor

comment:11 Changed 13 years ago by jburel

  • Description modified (diff)
  • Priority changed from minor to major

comment:12 Changed 13 years ago by jmoore

  • Milestone changed from OMERO-Beta4.3 to OMERO-Beta4.2.2

comment:13 Changed 13 years ago by jburel

  • Milestone changed from OMERO-Beta4.2.2 to OMERO-Beta4.3

comment:14 Changed 13 years ago by jburel

  • Description modified (diff)

comment:15 Changed 13 years ago by jburel

  • Description modified (diff)

comment:16 Changed 13 years ago by jburel

  • Cc s.hutten@… A.Visvanathan@… added
  • Description modified (diff)

comment:17 Changed 13 years ago by jburel

  • Description modified (diff)

comment:18 Changed 13 years ago by agilo

  • Status changed from new to accepted

Updated status, related task in progress

comment:19 Changed 13 years ago by jburel

  • Milestone changed from OMERO-Beta4.3 to Unscheduled

comment:20 Changed 12 years ago by jburel

  • Owner changed from dzmacdonald to jburel

comment:21 Changed 11 years ago by jburel

  • Resolution set to fixed
  • Status changed from accepted to closed
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