9:50 A – 7:30 P, 8:30 P – 10:50 P
General
- Discussing replies for Banff invites.
- Student substitutions add to bottom of list
- Still need to write more acknowledgement of replies.
STORM Analysis
- launch analysis of all unprocessed datafiles.
- ESATA connection (maybe connection in general) slows DRAMATICALLY when trying to read data to two computers at once (attempted one batch processing on Monet and another round of processing on Tuck).
- Happily runs multiple analyses in parallel on TUCK. Unusable on Monet during analysis — this is definetely worse with ESATA than USB.
- USB connection to Alistair8 working better. system does stall occassionally and needs a kick — opening and closing the hard-disk in windows explorer on Monet seems to get ti rolling again sometimes. Not really sure why this analysis goes in spurts. At least system does not freeze when working over USB.
- editing a file on a stalled/lagging disk seems to wake it up and kick-start the analysis again. Tuck back at full speed analysis.
- Restarted analysis on Alistair8\2013-02-14_BXC2color\STORM\BXC_storm_488_0001.dax. Check if these files have any data in frames 500-1500, analysis picked up where it left off but sent a warning that file appeared empty. Might have lost earlier localizations.
- Slow reading / analysis stalling might be aggravated by having too many separate files trying to read and write at once (seems to be stalling Cajal now with more batches going). Try smaller batch size and see if this helps.
- Not really sure if batch size makes difference. Having multiple computers access and read the same hard-disk does seem to increase the stall frequency though.
- Should really start copying data over to Odyssey and running there.
- Running analysis of remaining data from Alistair8 O/N on Tuck and Cajal. (02-06-13 data is only processed by insightM, still need DaoSTORM).
- Should run a few more datasets in InsightM as well for comparison.
- current InsightM counts at least from 02-06-13 BXC Pc-488 data not very good in either channel.
Bead fitting issues
- 3D bead fitting is definetely underestimating bead spread. I have no idea why this should be, it ‘thinks’ the z-stack beads go through the full range of -600 to 600, I don’t know why it should then map the chromatic calibration alignment beads to a narrower profile.
- open problem still.
Coding
- Fixed some bugs in STORMrender
- Improved some menu options default handling in STORMfinder
Embryo section staining
- AATAT control works great.
- BXC probe fails again (and we’re out). Should have tried it on cells as a second check.
- Preparing AATAT samples to troubleshoot some more antibody staining. Attempting En stain, H3K9me2 (abcam m), and H3K27me3.
- Thawing another coverslip to attempt straight abdB staining.
- AbdB staining fails
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- maybe we can we do sequential imaging (all in cy5!). Embryo sections are pretty distinctive and only a few on an individual slide. Might be easier than doing the multiplex.
- Updating embryo sectioning results:
Discussion
- Ke tracks beads during image acquisition as well as before and after.
- Does not use dual/view quadview
- manual (not-motorized) filter wheel.