Wednesday 02/25/14

10:30a – 11:00p

Chromatin Project Analysis

Analysis of multi-color data

  • quick look at G1-G2 data from 12-30. Almost complete overlap of regions.

Current multi-color / adjacent region datasets:

  1. ‘Q:\2014-01-10_F11-7_F12-6’
  2. ‘Q:\2014-01-10_G01-6_G02-7’
  3. ‘Q:\2014-01-09_F05F06’
  4. ‘Q:\2013-12-30_G1G2’ – 750 survived remarkably well. Should check buffer on this
  5. ‘Q:\2013-12-28_F12F11’
  6. ‘Q:\2013-12-27_F12G01’
  7. ‘T:\2014-02-12_F05-6_F06-7’ – buffer died amazingly fast (in 1/2x BME?)
  8. ‘T:\2014-02-15_F06-6_F05-7’ – buffer died amazingly fast (in 1/2x BME?)

New staining

  • plate and fix cells
  • check cell density (just passaged yesterday, so this may not work).
  • density looks workable. Prepped for staining
  • new stains:
    • F06 A647 + F05 A750 (rpt, lower conc. hopefully better buffer)
    • F04 A647 + F05 A750
    • F03 A647 + F04 A750

code updates

  • added resolution option to STORMrender
  • substantial changes to ChromatinCropper in making it multicolor with new methods.
  • Ncolor still giving a little bit of trouble with colormaps when toggling active channels on and off.
    • when mlist is 1 dimension / 1 active channel the image is 2D and then Ncolor uses the colormap passed as the color range for the single color. So the 2nd active channel works fine but when only the first channel is active things screw up.
    • typically for multicolor images I’m passing Ncolor the hsv(2) or hsv(4) map. But for single color I use hot(256).
    • I’m sure I’ve made this somehow more complicated than it needs to be.


  • project 2 planning (see notes)
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