Wednesday 03/27/13

10:00 A – 7:00 P, 9:30 P – 12:20 A

STORM

• Break down O/N STORM run on STORM3 of fab7-405-cy5
• STORM2 has issues
  1. Iris for columnating optics is too small for 512×512 view
  2. Focus lock can’t get minimal signal
  3. TIRF field is not flat — suggests back-optics alignment is off.
• STORM2 fixed
  1. focus lock issue was due to
  2. Aligned to 512×512 field of view. Iris unscrews (just close all the way and keep screwing)
• Setting up sample 1 (2x cy5) on STORM2 for imaging

Review writing

• Working on intro
• Need to add He2010 discussion and citations
• Not hyperbolic response (traditional site occupancy) if enhancer breakdown allowed.
  

Stuff

• Help Jiang with colocalization (JiangClusterAnalysis, in Image_Analysis code folder).
  1. Review local maxima tricks from stackoverflow
  2. Straight imregionalmax and pic > imdilate(pic ...) pretty sensitive to image noise.
  3. Combined with a little gaussian blur gaussblur = fspecial('gaussian',5,2); pic = imfilter(in,gaussblur,'replicate'); And a little thresholding, imregionalmax does pretty well.
• Passport renewal application
• Listen to Dianne’s message and write back by email