User Story #3358 (accepted)
HCS in client
|Reported by:||jburel||Owned by:|
|Cc:||mlinkert, wmoore, bzloranger, ajpatterson, cblackburn, jamoore, jrswedlow||Story Points:||n.a.|
|Total Remaining Time:||0.95d||Estimated Remaining Time:||n.a.|
Description (last modified by jburel) (diff)
The HCS facility in Dundee, HUT and ourselves have started a collaboration to look at improving the analysis of HCS data in OMERO.
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.
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.
- Marking images with a certain interesting phenotype(tagging)
- More ways to mark classify cells, (Namespaces)
- store results in OMERO.tables:
- 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.
Currently we have very basic cellprofiler integration in OMERO
- Cc mlinkert-x, wmoore, bzloranger, ajpatterson, cblackburn added
- Milestone changed from Unscheduled to OMERO-Beta4.3