Thursday 05/01/14

8:30a — 11:00p

OligoArray development

writing new batch processing functions to run OligoArray with sbatch on Odyssey.
encorporating new functions into matlab-functions.
Pulled matlab-storm, matlab-functions, and storm-analysis repositories into my remote folder on Odyssey /n/home05/boettiger/
debugging remote OligoArray launcher. A bit cumbersome editing in local repository and push/pulling through github.

O/N run completed successfully, but 405 laser was off. Hence insufficient swithcing.
Examining 750 samples
- G3-p4 750 staining evident in every cell (though weak / low contrast high background). Maybe just need less secondary, I know this primary alone looks good. Oddly the G2-p1 647 looks worse than usual.
- 750 staining not that detectable in G08-p3 sample. Background high. G06-p1 staining does not look nearly as good as in previous stains. Maybe I should go and re-image those G06s soon, I think the only data I currently have from G06 missed the RNase digestion.

ChromatinCropper of C02 data. Data is pretty noisy, I suspect bad switching contributes. may want to restain and reimage.
analyzed through image 18 (30+ loci)
analyzed E01 data from truncated STORM1 run. Actually pretty decent switching
analyzing E01 data moved to STORM2. Should have replaced buffer — spots look fantastic but sparsely sampled. Not enough switching. Movies much to short as well compared to expected length for a 250kb (yellow) region. Should get ~125+ frames of good switching for a region of this size.