| | 1 | The HCS facility in Dundee, HUT and ourselves have started a collaboration to look at improving the analysis of HCS data in OMERO. |
| | 2 | |
| | 3 | = Current situation = |
| | 4 | == Visualisation == |
| | 5 | |
| | 6 | Currently the HCS group has a workflow that seems to be a reasonable starting point for us to incorporate into OMERO: |
| | 7 | * Tracking Reagents, links to a reagent library used on Plate |
| | 8 | * Marking plate to determine what reagents was used on well |
| | 9 | * 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. |
| | 10 | * Quite often the acquisition time of the image is quite short and so the intensities are very low. |
| | 11 | |
| | 12 | == Analysis == |
| | 13 | In many cases the HCS facility did very basic analysis: |
| | 14 | * 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. |
| | 15 | * Some metrics are calculated on images: cell count, mitotic index |
| | 16 | * No real analysis occurs on these metrics |
| | 17 | * Often they do not look at images very closely, and so miss interesting phenotypes, distributions. |
| | 18 | = HCS Workflows in OMERO = |
| | 19 | |
| | 20 | It seems reasonable that we should try to incorporate, and improve on the available workflows and analysis in OMERO. |
| | 21 | = Visualisation = |
| | 22 | * Marking images with a certain interesting phenotype(tagging) |
| | 23 | * More ways to mark classify cells, (Namespaces) |
| | 24 | * store results in OMERO.tables: |
| | 25 | * view |
| | 26 | * graph |
| | 27 | * compare |
| | 28 | |
| | 29 | = Analysis = |
| | 30 | * Calculate basic metrics that already exists |
| | 31 | * Calculate new metrics: |
| | 32 | * Cell density |
| | 33 | * Phenotype identification, supervised(more like this), unsupervised |
| | 34 | * Cell distribution on the well, for instance in epithelial cells. |
| | 35 | * Display of analysis results: Heatmaps, graphs, other methods of interrogating data. |
| | 36 | |
| | 37 | == !CellProfiler == |
| | 38 | Currently we have very basic cellprofiler integration in OMERO |
