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- Timestamp:
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03/11/10 12:33:59 (14 years ago)
- Author:
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dzmacdonald
- Comment:
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Legend:
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initial
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v1
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| 1 | 1 | In collaboration with the BioInformatics group in Dundee we will add FLIM functionality to OMERO. |
| | 2 | |
| | 3 | == Current Workflows == |
| | 4 | |
| | 5 | Currently users using SPCImage have to go through a number of steps to generate their analysis results. |
| | 6 | |
| | 7 | 1. Draw an ROI around region of interest (cell, part of cell, cell cycle) |
| | 8 | 1. Perform analysis in SPCImage |
| | 9 | 1. Select cut off for k1 |
| | 10 | 1. output results to excel where the k1, k2 values are transformed in to E'fret conditon, (1-k1/k2*100) |
| | 11 | 1. Generate heat map from E'fret, each map must have min, max set by hand |
| | 12 | 1. Repeat for each region of interest |
| | 13 | 1. Combine results to get averages for different treatments, cell cycle. |
| | 14 | |
| | 15 | Typically a user will generate 100 fret images per day, each days aquisiton can take up to 2 days to analyse. |
| | 16 | |
| | 17 | == OMERO Workflows == |
| | 18 | |
| | 19 | 1. In OMERO the user should be able to draw the ROI in different regions on the image |
| | 20 | 1. select the fret, no fret images |
| | 21 | 1. Run analysis |
| | 22 | 1. Generate the Heatmaps and upload/attach in OMERO |
| | 23 | 1. Generate the summary results |
| | 24 | 1. Allow the visualisation of the chi value to see how good the fits are. |
| | 25 | 1. Allow thresholding on chi value to remove from heatmap |
| | 26 | |
| | 27 | This will save users many hours of copying and pasting from SPCImage to Excel, and then Excel to other graphing software. |
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