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
      • vlist
      • imaxes
      • impars
      • 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.
      • daxfolder
      • binname
    • its dot quantification statistics
      • Area
      • 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
      • use 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
      • Area

Experiment planning

Imaging Priorities

  • G05 647
  • D12 647

Staining Priorities

  • F03 + F04
  • F05 + F04
  • G01 + G02
  • G01 + G02 + G03
  • G01 + G02 + G03 + G04
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