Monday 02/03/2014

10:00a – 11:50a


  • Hao practice talk for lab meeting, 11a – 1p.
  • Tamara’s seminar at the stat depart colloquium, (see notes)

Ph Project

manuscript work

  • working on re-arranging figure panels and colors
  • added whole cell images to figure 2
  • added more zoom-ins to figure 2
  • introduced color conventions — each protein has a unique color. General color map is red to cyan.
  • started working on rewriting modeling section text.
    • Should be written from ground up
    • Need to make it clear from topic sentence what the objective to test is (Ajaz has a good start for this I think), and then clearly state the two specific alternative hypothesis we will test through the model and its comparison to our data.
    • Probably need to redo ‘fraction clustered’ in terms of new cluster diameter framework.

data collection

  • continue imaging WT-Ph-flag + Psc
  • take bead images
  • start imaging M-Ph-flag + Psc
  • Dave not talking properly to hal? STORM2 dave generated run file says to record 25,000 frames of 750. I come back two hours later and it’s still recording frame like 2 million+ of the first 750 movie. Not inspiring.
  • Restarted imaging run. Seems to be working smoothly.

Chromatin project

STORM Imaging

  • finish imaging ANTC. Lost focus at position 3 last night. :(. Reset focus and increased IR laser strength for focuslock.
  • focus successfully maintained for a few more images (10a – 1p).
  • realign camera and microscope. Camera removed today for use on STORM4-dual objective.
  • image G01 G02 data on STORM4. Very good staining, very good switching. imaging 90K frames (could probably do more, but that’s most of it at least). Little 405 necessary.
  • ISSUES with STORM4: GUI doesn’t actually update when switching parameters (for example, if the run shutters box defaults to be checked on a new parameter set, but not the current one, when you switch to the new parameter set the box will be unchecked. Nonetheless, it will still run as if it is checked. This problem is STORM4 specific.
  • More annoying: I can’t set the conventional images and STORM images to have different movie styles. I set one to .dax and one to .647 and it sets them both either to whichever I’ve set more recently. This problem is also STORM4 specific. The only code I know of that’s different is the default parameters are set to point to the STORM4 defaults.

Cell culture

  • passage cells
  • (need to flip fly stocks very soon, tomorrow if manageable).
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