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:
- Launching data corresponding to an acquisition of " No FRET conditions"
- Draw an ROI around region of interest (cell, part of cell (nucleus) , different stage of mitosis...)
- Determine background level
- Determine if it is necessary to increase binning by looking at the average photon count in the ROI.
- Perform analysis in SPCImage by applying a monoexponential decay model and fixing the background value.
- From the analysis of a single ROI, k no fret = k2 value is output in Excel.
- Repeat this analysis of each ROI of a picture and then for n acquisitions of the " No FRET conditions"
- Save intensity image as tiff; save k no FRET map as tiff
- Calculate a k no fret= k2 average value from the n k2 values analysed.
- Launch data corresponding to an acquisition of " FRET conditions"
- Draw an ROI around region of interest (cell, part of cell (nucleus) , different stage of mitosis...)
- Determine background level
- Determine if it is necessary to increase binning by looking at the average photon count in the ROI.
- 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).
- 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.
- 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.
- Repeat this analysis of each ROI of a picture and then for n acquisitions of the " FRET conditions"
- Perform calculations in Excel (normalisation FRET populations, etc..)
- 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
- In OMERO the user should be able to draw the ROI in different regions on the image
- select the fret, no fret images
- Run analysis
- Generate the Heatmaps and upload/attach in OMERO
- Generate the summary results
- Allow the visualisation of the chi value to see how good the fits are.
- 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
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
Notes from discussion Mar. 11: