Monday 02/13/12

10:00A -7P, 10P-12:20A

  • Visiting postdoc talk (Bryan). 10A-1P
  • Flip fly cage 1P.
  • Some STORM stacks didn’t process in batchinsightm.  Some issues still in running code, tweaked code and re-running missing data sets: S45, S44ubx, Pc, S45_13i.
  • Working on image registration
  • NuGru meeting (Nicole presenting on PcGs across mitosis)
  • #Need to check mitotic nuclei for Pho and Su(Z)12
  • Colenso helps work out image registration: feature size 8, not 16.  Elastic registration. “Accurate” not “mono”, initial deform very coarse, final deform: very fine, divergence = 0.1, Curl = 0.1, Landmark = 1;   Works on test sample of 2 images from cy3B channel of s2en (2010-02-10).  Trying on rest of stack.
  • other recommendations: more WGA!  1:10 is much better than 1:20 in CS hands.  I’ve been doing 1:500 on current images and 1:50 in this weeks images.
  • Confocal imaging of sections embedded for cutting: immersion objectives bend coverslip, which prevents refocusing.  Built a reinforced coverslip which should resist bending, did not test out yet.
  • can see en exonic stripes clearly in red channel by eye with 20x air, and by confocal fast and slow scans.
  • can not see intronic hox gene expression by eye or by confocal slow scan.
  • nascent transcripts of hox genes clearly visible on slow (speed 2) scan with 20x air (for z stack) and 40x oil (not tested with reinforced slide).
  • Can mark embryo region with 10x, try circle and cut.
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