10:30a – 7:20p,

matlab-storm

STORMrender online

• Getting Jeff set up with STORMrender

debugging:

• 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).

Chromatin

New metrics

TADS

• 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.

STORM

• 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.