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.
STORM
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.
