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User Story #1970 (new)
FLIM in OMERO
— at Version 1
Reported by:
dzmacdonald Owned by:
dzmacdonald
Priority:
n.a.
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:
2010-03-05 (4)
Importance:
Exciter
Total Remaining Time:
0.0d
Estimated Remaining Time:
n.a.
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.
Draw an ROI around region of interest (cell, part of cell, cell cycle)
Perform analysis in SPCImage
Select cut off for k1
output results to excel where the k1, k2 values are transformed in to E'fret conditon, (1-k1/k2*100)
Generate heat map from E'fret, each map must have min, max set by hand
Repeat for each region of interest
Combine results to get averages for different treatments, cell cycle.
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
References
Referenced by:
← Requirement (#1924 ): Collaborations
References:
→ Task (#4256 ): Wrapper for script
(
Owner : dzmacdonald
Remaining Time : 0
)
→ Task (#4712 ): Upgrade Edinburgh Server
(
Owner : dzmacdonald
Remaining Time : 0
)
→ Task (#4713 ): Update Rapid to add new parameters
(
Owner : dzmacdonald
Remaining Time : 0
)
→ Task (#4711 ): Update FLIM script
(
Owner : dzmacdonald
Remaining Time : 0
)
→ Task (#3498 ): Testing scripts performance
(
Owner : dzmacdonald
Remaining Time : 0
)
→ Task (#4259 ): Submitting job via RAPID
(
Owner : dzmacdonald
)
→ Task (#4261 ): Script: support for new parameters
(
Owner : jburel
)
→ Task (#4257 ): Script: handle results.
(
Owner : dzmacdonald
Remaining Time : 0
)
→ Task (#4262 ): Script: IRF not required
(
Owner : jburel
)
→ Task (#3713 ): Save output of scripts
(
Remaining Time : 0
)
→ Task (#3700 ): Save image as separate
(
Owner : jburel
)
→ Task (#4205 ): SPC Image how to
(
Owner : jburel
Remaining Time : 0
)
→ Task (#4260 ): Results selection and comparision
(
Owner : jburel
)
→ Task (#3699 ): Replace min max
(
Owner : jburel
)
→ Task (#3589 ): Layout FLIM results
(
Owner : jburel
)
→ Task (#4846 ): Integrate graph and heatmap
(
Owner : jburel
Remaining Time : 0
)
→ Task (#1921 ): Integrate FLIM script
(
Owner : dzmacdonald
Remaining Time : 0
)
→ Task (#3270 ): FLIM: update script to talk to OMERO
(
Owner : dzmacdonald
)
→ Task (#3504 ): FLIM: launch script from insight
(
Owner : jburel
Remaining Time : 0
)
→ Task (#3647 ): FLIM: files annotations name.
(
Owner : dzmacdonald
)
→ Task (#3648 ): FLIM: background color in chart
(
Owner : jburel
Remaining Time : 0
)
→ Task (#1984 ): FLIM: Visualisation
(
Owner : jburel
Remaining Time : 0
)
→ Task (#3512 ): FLIM: Update RAPID
(
Owner : dzmacdonald
)
→ Task (#3272 ): FLIM: Testing
(
Owner : dzmacdonald
)
→ Task (#3271 ): FLIM: Submit job from RAPID
(
Owner : dzmacdonald
)
→ Task (#3645 ): FLIM: Stats display
(
Owner : jburel
)
→ Task (#3274 ): FLIM: Setup servers at Edinburgh
(
Owner : dzmacdonald
)
→ Task (#3637 ): FLIM: Save results
(
Owner : jburel
)
→ Task (#1985 ): FLIM: ROI tagging, storage
(
Owner : dzmacdonald
Remaining Time : 0
)
→ Task (#3646 ): FLIM: Order table
(
Owner : jburel
Remaining Time : 0
)
→ Task (#3101 ): FLIM: New flim script
(
Owner : dzmacdonald
)
→ Task (#3638 ): FLIM: Improve Save to Excel
(
Owner : jburel
)
→ Task (#3511 ): FLIM: Fix persistance issue with RAPID
(
Owner : dzmacdonald
)
→ Task (#3273 ): FLIM: Documentation
(
Owner : dzmacdonald
Remaining Time : 0
)
→ Task (#2867 ): FLIM: Create namespace on startup
(
Owner : jamoore
Remaining Time : 0
)
→ Task (#1972 ): FLIM speed optimisation
(
Owner : dzmacdonald
Remaining Time : 0
)
→ Task (#1807 ): FLIM script integration
(
Owner : dzmacdonald
)
→ Task (#2918 ): FLIM parsing IRF file
(
Owner : dzmacdonald
Remaining Time : 0
)
→ Task (#2914 ): FLIM error handling
(
Owner : dzmacdonald
Remaining Time : 0
)
→ Task (#3588 ): FLIM and viewer
(
Owner : jburel
)
→ Task (#1971 ): FLIM add optimisations to improve accuracy of curve fit.
(
Owner : dzmacdonald
Remaining Time : 0
)
→ Task (#4524 ): FLIM Wiki page
(
Owner : dzmacdonald
Remaining Time : 0
)
→ Task (#4710 ): Create a install script to make grid installation simpler
(
Owner : jburel
Remaining Time : 0
)
→ User Story (#4258 ): Color Results visualization
→ Task (#3662 ): Chart Display
(
Owner : jburel
Remaining Time : 0
)
→ Task (#4208 ): Bug: Interval table not refresh
(
Owner : jburel
Remaining Time : 0
)
→ Task (#2896 ): Add Threshold parameter
(
Owner : jburel
Remaining Time : 0
)
Change History (1)
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