Thursday 01/16/2014

9:30a – 1:00a

Happy Birthday.


  • Stain new cells: ANT-C, G05, D12
  • chromatin probe synthesis debugging
    • order new Maxima and T7
    • create list of probes to make next
  • start compressing bead data! – postponed again.

Chromatin Project

  • Finish O/N STORM of F04-A647, F03-A647
  • start analysis of F03,F04 and F04,F03 data
  • Finish running ChromatinCropper on F10 data
  • update and reboot Monet
  • Working on slides for next meeting with XZ: full Lib2 data update

Coding Genome analysis

  • adding gene viewer: GetLocusGenes.m
  • now built into the LoadKc167Data.m
  • Note current version of flip gene only flipped complete genes, not genes that edged into the region.
  • Fixed in GetLocusSenseSeq.m
  • constructed maps for all of Lib2

Coding matlab-storm

  • Multi-color display works fine.
  • single color loading of demo data fails.
  • fixed single color loading — imagesc won’t write indexed images (i.e. 2D matrices, not RGB data) to axes in a GUI (I just get a solid colored field. I can change the color, but not actually get the image). Sending the same command to the GUI handles.axes2; images(I); and to figure(1); imagesc(I) back to back in the same code produces the image correctly in the figure and as a solid field in the axes. As soon as the image is an RGB image it displays correctly in both. WEIRD matlab. weird.
  • (simple work-around, use ind2rgb(I,map) to convert first. Only it’s pick about the range of the map, the data type of the map (needs a double, even though you can call a color map on a uint16, it gives weird results). Also ind2rgb takes uint16 but returns double, which doesn’t seem obviously scaled, so I use makeuint to convert these to balanced contrast uint16.
  • at some point I want to get rid of the automatic balanced contrast, or make it a toggleable function rather than an intrinsic property.


  • ordered new Maxima (full length)
  • ordered new T7 kit
  • ordered new ProRAID (4 bay) — easier to fit on desk, no adventage with 8 bay sincy they max out the RAID 5 array at 4.
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