8:00 am – 5:00 pm, 8:00 pm – 9:45 pm
Goals
- revise domain names to match new conventions
- write 100 word summary for paper.
Meetings
- lab meeting
- discuss microscopes
- group C presentations
- microscope decisions
- buy new Andor 897 ultra for STORM5
- buy new 750 laser (MPB if they can promise time) for STORM5
- buy new 1-2W 561 laser (MPB) for STORM3
- I will help CX install new camera and quadview and set up 3D imaging on STORM2.
MERFISH coding
- working on converting new approach into a discrete function based pipeline of code
- plan to wrap these functions into a GUI as well.
- Additional approach: using blanks formally in a machine learning context to discriminate real spots from background
- we have examples of what we know for certain background looks like, and examples of stuff we think is signal but may include background.
- we can set a false positive tolerance (number of background counted) and chose the discriminator that maximizes detection while meeting this required false positive.
- current approach does completely independent cuts on total brightness and brightness ratio (two highly correlated quantities). Could compute the proper 2D (or ND) seperator between
Manuscript
To do:
- need to address JM’s outstanding comments
- got feedback from BB — some recommended reference changes. Need to add
- go feedback from GF and MI — some recommended reference additions. More with LM’s comments.
Computer observations
- Tuck and Cajal very slow after logging into terminal
- suspect windows / dropbox syncing configuration is slowing things down (?)
- Cajal when run at terminal just seems painful. Graphics card communication issue?