Saturday 01/04/13

10:00a – 11:55p

(sailing canceled do to malfunction of committee boats)

coding matlab-storm

  • RunDotFinder “skip existing” option on DaoSTORM I believe is interpreted as resume and in insightM as actually skip. This should be double checked and made clearer. Maybe we want a legitimate skip as well to be an option for DaoSTORM.
  • Fixed up alternate binname functions (can pass it 'DAX' to include the current daxfile name and append or prefix it with a new id. Can also pass it '#' to insert image index (based on results of dir daxroot).

Mostly writing new multi-region version of ChromatinCropper

  • Not all movies have bead data analyzed yet (I suppose I was planning to downsample all these files. I should probably set that up to run soon).
  • note with no averaging and single round, daoSTORM seems to out perform insightM on bead-data
    DevelopingCC2

important observations in drift correction

  • smoothing may work alright, but has serious issues at the boundaries. We use these boundary points to correct drift between movies, so this is an issue.
  • we could compute a warp based on the bead images.
  • fixed NaNs is fastsmooth.m (rather than using inpaint_nans.m, both from Matlab file server). Original author had tried to make it NaN friendly but got foiled by the + and - operators which still return NaN. (use nansum([a, -b]) rather than a - b to subtract and ignore NaNs).
  • also switched to narrowed averaging window rather than just zero padding of ends during smoothing.
  • still need to do something about vibrating beads.

STORM analysis

  • Bead data from F12G1 not analyzed. Processing now on Cajal
  • no data from G1G2 analyzed yet. Processing now on Cajal
  • G1G2 data not nearly as bright as other data sets. Should collect more data with a fresh buffer when we get 750 time again.
  • G1G2 slide is pretty low density on beads — lots of images have none.
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