Monday 03/24/14

10:00a – 11:15p

Chromatin Project

Data summaries

  • making slides to summarize recent analysis of multi-color data
  • see slides for 3/28/14 XZ meeting

Data analysis

F03-F04 data

  • chromewarps obviously don’t match data, clear multi-pixel shift up and to the right on all spots


  • Split up the many steps of CalcChromeWarp into separate functions (finally) so that they can be used independently.
  • This still needs some improvement given current variable names / data storage formats, but its a step in the right direction.
  • modifying ChromatinCropper to change warp files via the Menus and ‘remove last blob’ via menu commands.




PRISM2 coding

  • branched off from prism2. Pulled daxwriter-master (pushed up from STORM4) down into new branch.
  • New version of Dave won’t work with Steve until Steve is brought up to speed with new TCP protocol communication method
  • updated steve-settings using the prism2 branch defaults.

imaging observations

  • imaging C02 sample on PRISM2
  • using Cy5Cy3 3D dualview insert.
  • laser beam needs some alignment, not too bad, I’ll just use it as it is today
  • system loses focus — offset will got to -1300, and stay there, despite lock target set at 0.
  • molecules quite dense (high background?) and staying on for multiple frames (higher laser power would really be nice).
  • IR focus lock sum signal varies between cells. This system has high sum signal values (0 – ~1600? instead of 0-255).

Genome patterns

  • enhancers don’t cross boundaries – example brk enahancers inside likely contiguous yellow domain flanked by likely blue / black regions.


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