Tuesday 03/12/13

10:00A – 11:15P

STORM

Finish O/N STORM run on STORM2
Finish O/N STORM run on STORM3
Installing mount and sliders on STORM4 to allow for 3D imaging
Lessons:
1. Final appeture (removed for alignment) front-back position chosen to minimize the size of the spot on ceiling.
QV2 alignment for the Quadview not clear. ( = Colenso’s answer)
1. “First align to ccd aperture”. And then all the rest? Or no? = YES. These guys not so important
2. “Then switch to QV2 mode and adjust left,right” adjust the L/R ccd appetures? Or the QV2 appetures? = QV2 appatures, these are key
3. Centered beamspot on camera. Add in quadview, make straight/flush with microsocope. Beamspot NOT centered.
Aligning with Colenso:
1. Use brightfield to align quadview first, center such that there is no clipping, that QV is square, follow QV Alignment (now on desktop).
2. Lock down camera, then align back-optics.
Setup O/N STORM run of slide 6: 2xCy5-405 Fab7 to run on STORM2

Downloaded and installed BLAST+ (to default Program Files location)
Reading and trying to understand Jeff’s PickPrimers_031213.m and Oligopaint_FindPrimers_031113.m scripts
Reorganized Data folder: Genomics main directory, subdirectories for Human and Drosophila genome files, subdirectory for genomeTracks, sub-directory for oligopaint, and subdirectory for PrimersEtc.
Will need to update these paths in my bioinformatics scripts
Downloaded chrX as Fasta and genbank file
Downloaded rest of Dmel chr as Fasta
constructed combined FASTA for Dmel genome
used Jeff’s matlab script to locally BLAST Jeff’s primer set against the Drosophila Genome (see Blastprimers.m)

Copying data from Alistairtemp to Alistair9 (780 GB). Hopefully this completes before my STORM3 session — estimate not looking good.
Alistair9 2013-02-17_fab7_ss parameters configured for DaoSTORM analysis
cleaning Git repo on Cajal and Tuck
Installing Matlab2012b on Cajal
Move External folder back into Cajal Tuck local repositories so that STORMfinder can actually run.
Analyzing Fab7_647 SS_488 data on Cajal
Drift is substantial. 10,000 frames of un-analyzed positions during which to acrue extra drift. Try analyzing these frames and seeing if that fixes things.
seems to be an issue with Global drift correct.