Sunday 03/30/14

Posted on March 30, 2014 by admin

10:40a – 12:15a

Some basic organization

matlab-functions collaboration

  • discussed plans
    • make headers match more strictly
    • move all user prompts to pop-up boxes not command line prompts

Project organization folder structure

  • change all scripts folders to short-cuts or symbolic links to the GitScripts folder.

Backups

  • pushed GitScripts

Chromatin Project stuff

Cell staining

  • rinse out primaries from E01-E03 stains
  • move to 4C, will image tomorrow night.

Chromatin Analysis

Analyzing F03-F05 data from 01/17/14

  • overall data looks pretty good
  • some alignment / drift / conventional-storm registration issues at cell 8 or 9.

Analyzing F04-F03 data from 01/15/14

  • some cells look pretty good
  • 750 counts drop pretty rapidly after the calibration movie.
  • some cells have clear alignment mismatch / drift issues. See conv vs STORM:
    clearAlignmentError

Data so far

  • exploring new plotting options
    • violin plots for matlab — somewhat useful.
    • also interesting, distributionPlot. Added to my FromFileExchange functions.
  • some comparisons between blue-blue, blue-yellow, and black-yellow

ViolinPlots
QuantOverlapChromatin

Ideas for further analysis

  • screen through good 3D data, provide 3D overlap analysis.
  • Surprising trends from 3D analysis

surprising3Dtrends

Ph Project, to do:

  • Make supplement image of antibody controls
  • write caption for supplement image of antibody controls
  • remake supplement figure on counts vs. diameter to capture new standards (now it’s own proper figure script).
  • write caption for supplement image of molecule counts (instead of diameter) – complete
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