9:45 A — 5:20P, 8:30P — 11:50P
- Finish STORM O/N of S45 (13-introns)
- setup STORM run of Pc
- Flip fly cage (10:50P)
- Flip fly cage (1:50P)
- Hal holds control of 647 laser AOTF against labview. Fixed.
- Analyzing STORM data by batchinsightM: H3 data (panH3 and H3K27me3).
- Fix embryos (3:20P) (1.5-5hr collection)
- # Flip collection cage 4:50P
- Some files fail to run in batchinsightM. Issues identified with hazen: spaces matter. safer to join multiple inputs to the command line as [A,B] than A + B. If .dax files exist that don’t match one of the inputs (e.g. movie.dax not fit 647storm.dax, system throws an error. Wrote version to avoid this. Could write a default ini file but risk generating molecule lists for uncalibrated files.
- Analyzing remaining STORM data from Friday and Saturday night
- working on summary of Confocal vs. STORM results to date for recent experiments to enter into notebook (see posts).
- New antibody test summary: 15 min fix Psc, Pc, Pho and Su(z)12 all work. dMBT still not working.
- Acetone fixation completely failed to devitlinize embryos. Consequently no staining.
- Testing of new resin (slow to cure, 20 hours to turn into a plastic, still squeezable soft at top.
- Thin sectioning of traditionally mounted H1 sample — very thin sections. compressing? or just trimmed really thin?
- Attempt to trim block of H1 sample — surface is not smooth. Does not trim well.
- Confocal of untrimmed blocks: working distance of 63x a bit too small: can see but no ability to focus up down. Not sure why I can focus on mid-sagital plane and nothing else.
- 20x air objective with water between plastic and glass coverslip works fine for imaging. Excellent nuclear definition in 647 channel. 561 looks more backgroundy in solid resin. 488 can just resolve nuclear membranes in WGA.