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.