Saturday 01/18/2014

10:30a – 7:20p,


STORMrender online

  • Getting Jeff set up with STORMrender


  • STORMfinder added paths in initialization, allowing matlab-storm to access depreciated versions of code in folders that weren’t supposed to be on filepath

Features to add to STORMrender

  • user defined colors
    • make a little RGB GUI, enter 3 numbers, show a swath patch of the color
    • automatically populated with each of the loaded channels (STORM, overlays, Z-colors per STORM).
  • automatic auto-contrast for overlays

Bugs to address

  • log-scale tick box doesn’t work
  • Levels doesn’t automatically populate until you select the slider.
    • Should trigger the update triggered by dropdown menu selection when the image is loaded.
    • This should happen for overlays as well as STORM images (though I guess you never just load an overlay).

Learning Matlab Debugger

  • when stopped in debugger, matlab workspace changes to be inside the function.
  • step just progresses to the next evaluation statement.
  • step-in opens internally called functions, opens these functions in editor and lets you see their workspace
  • add new breakpoints and hit continue to run through loops etc (don’t want to step through these one at a time).


New metrics


  • numTADs is not so useful (just counting boundary domains, BDs). Some domains are essentially all a single TAD and happen to pick up one or a pair of TAD boundaries at each end of the domain.
  • really want a weighted sum. e.g. 5 TADs of equal length should score a 5. 5 TADs dominated by 1 big domain and 4 tiny ones should score close to 1.


  • reimaging of F04-647 F03-750
  • confirmed switching is much better in MEA, should repeat imaging this locus
  • too late at night now to set up run (1:00a).

4C broken again. Up to 11.6 C. Waiting for maintenance to arrive.

Ph Project

  • staining Pc cells and new antibody-screen cells with Dm01-488 to help address the nuclear / cytoplasmic issues.
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