Chromatin Project, short-term goals
Issues with current data analysis
- In trying to get of order 100 loci per chromatin domain I’ve take a bunch of partially imaged edge of focus domains or other less well defined images (e.g. near edge of field of view). These un-necessarily blur out the size distributions of regions. A more stringent filter will be better.
- I think this is maybe even more important for statistics like moment of inertia and total localizations
- I haven’t used the z-scan information for number of dots per cell. This is pretty important. We should make this a field of the export data so that each spot has
Changes to make moving forward
Better Data Filtering
- Let’s get Z information and other quality metrics into the chromatin cropper.
- Let’s plot the spots statistics on a scatter plot so we can see where each of them go
Better Data storage
- the two to three step annotation process is unnecessarily slow. This should all be done in the Chromatin Cropper
- Each individual dot should save
- its raw data
- imdata (Iconv, Istorm, Itime, Ihist XY YZ XZ, Icell, Iarea). For just that dot
- its ID information
- region ID (e.g. F03). This can be used to retrieve locus size, locus coordinates, ChIP seq details etc.
- its dot quantification statistics
- Area Map
- moment of inertia
- something like distance of local maxima from edge. Distance of internal local minima from edge. Define maxima/minima based on quantiles. Say local max are all the spots that hit 90% or above. Local min are all the local min that remain if we saturate 10% max and above.
- Coefficient of variation for localizations per pixel
- Water-filled areas
- png images
export_fig.m function with
set(fighandle,'PaperPosition',[0,0,width,height]). This will capture the
set(gcf,'color','k') and other properties, and preserve the spacing.
- conventional and STORM dot pair. Just re-apply an auto-contrast for the conventional image and then convert to the correct colormap. STORM image may require manual contrast adjustment
- F03 + F04
- F05 + F04
- G01 + G02
- G01 + G02 + G03
- G01 + G02 + G03 + G04
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