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User Story #3358 (accepted)

Opened 13 years ago

Last modified 13 years ago

HCS in client

Reported by:	jburel	Owned by:
Priority:	major	Milestone:	Unscheduled
Component:	Insight	Keywords:	n.a.
Cc:	mlinkert, wmoore, bzloranger, ajpatterson, cblackburn, jamoore, jrswedlow	Story Points:	n.a.
Sprint:	n.a.	Importance:	n.a.
Total Remaining Time:	0.75d	Estimated Remaining Time:	n.a.

Description (last modified by jburel)

The HCS facility in Dundee, HUT and ourselves have started a collaboration to look at improving the analysis of HCS data in OMERO.

Current situation

Visualisation

Currently the HCS group has a workflow that seems to be a reasonable starting point for us to incorporate into OMERO:

Tracking Reagents, links to a reagent library used on Plate
Marking plate to determine what reagents was used on well
Viewing: They view data in split view but when the image is bigger than a window the viewport covers the same area of each channel. When watching the user this made more sense, it was easier to see which part of each channel aligned.
Quite often the acquisition time of the image is quite short and so the intensities are very low.

Analysis

In many cases the HCS facility did very basic analysis:

One channel had tagged the element they were interested in and all they did was look to see if the item of interest was less/more or shaped differently. Commonly they just looked to see the image has lower intensity.
Some metrics are calculated on images: cell count, mitotic index
- No real analysis occurs on these metrics
Often they do not look at images very closely, and so miss interesting phenotypes, distributions.

HCS Workflows in OMERO

It seems reasonable that we should try to incorporate, and improve on the available workflows and analysis in OMERO.

Visualisation

Marking images with a certain interesting phenotype(tagging)
More ways to mark classify cells, (Namespaces)
store results in OMERO.tables:
- view
- graph
- compare

Analysis

Calculate basic metrics that already exists
Calculate new metrics:
- Cell density
- Phenotype identification, supervised(more like this), unsupervised
- Cell distribution on the well, for instance in epithelial cells.
Display of analysis results: Heatmaps, graphs, other methods of interrogating data.

CellProfiler

Currently we have very basic cellprofiler integration in OMERO

References

Referenced by:

← Requirement (#4270): HCS Support improvement
References:
→ Task (#7807): Well annotation → Task (#3980): Validate screen import selections ( Owner: cxallan Remaining Time: 0 ) → Task (#3998): ScanR plate dimensions not always correct ( Owner: mlinkert ) → Task (#3999): ScanR channel counts not always correct ( Owner: mlinkert ) → Task (#3871): RFE:Image should show Field/Well parent ( Owner: jburel Remaining Time: 0.75 ) → Task (#3359): Projection dialog is only dataset aware → Task (#3993): Populate PlateAcquisition ( Owner: mlinkert Remaining Time: 0 ) → Task (#3994): InCell well names are not always correct ( Owner: mlinkert ) → Task (#3995): InCell image data not always correct ( Owner: mlinkert ) → Task (#3691): InCell 2000 data handling ( Owner: cxallan Remaining Time: 0 ) → Task (#3996): Improve InCell plate name population ( Owner: mlinkert Remaining Time: 0 ) → Task (#3360): HCS_PREVIEW generic build has wrong dir inside → Task (#4471): HCS spatial view: grid view ( Owner: jburel Remaining Time: 0 ) → Task (#4017): HCS spatial view: grid size ( Owner: jburel ) → Task (#4472): HCS spatial view: check position ( Owner: jburel Remaining Time: 0 ) → Task (#3361): From plate, method to display only images with measurements would be nice → Task (#3992): Decide whether to split BD Pathway fields ( Owner: mlinkert Remaining Time: 0 ) → Task (#3991): Decide how to color channels with identical wavelengths → Task (#3997): Cellomics reader does not populate SPW metadata ( Owner: mlinkert Remaining Time: 0 ) → Task (#3702): Better handling of large tables ( Owner: cxallan Remaining Time: 0 ) → Task (#4209): BUG: Browsing SPW - Preview ( Owner: jburel ) → Task (#3362): Apply to all for plate hangs app → Task (#3382): Allow visualizing multiple plates → Task (#4057): Adding annotation to Plate Acquisition ( Owner: jburel )

Change History (7)

comment:1 Changed 13 years ago by jburel

Description modified (diff)

comment:2 Changed 13 years ago by jburel

Cc jmoore jrswedlow added

comment:3 Changed 13 years ago by agilo

Status changed from new to accepted

Updated status, related task in progress

comment:4 Changed 13 years ago by jmoore

Status changed from accepted to new

comment:5 Changed 13 years ago by jmoore

Cc mlinkert-x wmoore bzloranger ajpatterson cblackburn added
Milestone changed from Unscheduled to OMERO-Beta4.3

This story has several tickets in the current milestone, so moving it to 4.3. Are the tasks in the appropriate sprints?

comment:6 Changed 13 years ago by agilo

Status changed from new to accepted

Updated status, related task in progress

comment:7 Changed 13 years ago by cxallan

Milestone changed from OMERO-Beta4.3 to Unscheduled

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