Thursday 09/06/12

9:50 A – 10:00 P

  • InsightM overloads Tuck from O/N data analysis. Canceled all further submissions to que to allow memory / CPU to free up for other users during the day.
  • InsightM also crashing itself due to memory overload as active tasks (including more full movies rather than conv and calibration images run O/N) are in process and accumulating large molecule lists.   Canceled another dozen processes, memory use scaled back to 80% RAM, 80% system CPU.
  • # Need to modify run insightM.m script to default to skip files which already have a _list.bin file when code is launched.
  • Etching coverslip 2 of S10: en,E(Pc) K27 H3.  20 min etch some sections start showing embryo outlines amidst some resin, other sections still show mostly resin.  Etching for another 30 min.
  • Still see resin, etching another 26 min
  • Fixed error in fxnZcal, added 2d error measurement export to bead-warp.   FxnZcal bug in finding frames at stage 0 and frames at stage max/min was causing z-calibration routine to error or give very bad calibration parameters which screwed up 3Dbeadwarp.
  • annotated fxnZcal so it is now more readable, understand what each section does.
  • More memory errors on tuck.  Files also running pretty slowly, probably saturating the USB and building up many large molecule lists to keep in memory simultaneously for a long time while waiting for the usb2 to transfer the data back and forth?  Stripped down to running just a few versions of insightM.
  • Another hour of etching (2 hrs total so far) still leaves ‘etching holes’ in most embryos where a bright ring appears ontop of the embryo of fainter color, presumably this part of the embryo is etched and the surrounding environment is not.  Etching for another hour.
  • Making saturated sodium meta-periodate solution.  6 scoops of powder and 15 mL of H2O, heated to 95C.
  • O/N confocal imaging of sogPr minus prox (m113).  Nice embryos.  Run started at 7PM.
  • Issues with stage focus, restarted run at 10PM.
  • STORM imaging of E(Pc) en K27 H3.  E(Pc) and 750.  750 switching great.  E(Pc) stain looks good.  K27-647 not switching well in many embryos (resin issue?)  en-488 not visible in any embryos.
  • regions with ‘holes’ seem to less bright, maybe switch less even than regions without? At least seems so in 750.  Probably could have etched much less then?
  • O/N STORM imaging of en.   lost focus on third movie.  Reset, but may lose focus-lock again.
  • O/N incubation of centromere-STORM coverslip and en coverslip in saturated sodium meta-periodate.

 

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