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.