Thursday 10/24/13

8:40a – 6:20p, 11:30p – 12:55a


  • Fix Ph model — neigbhors of neighbors
  • in situs day 2

Cell Staining

  • Hot washes (20 min, 2x 9 min in oven + 1 min switch)
  • 1x SSCT cold wash
  • PBT wash
  • 45 min lamin-488 stain
  • PBS wash
  • back to SSC

Ph model

  • Problems: Moving any attached molecules as a block doesn’t let flat sheets fold up.
  • Aborted development of 131024b Neighbor’s neighbor’s all part of same sheet.
  • New approach, single bond at a time
  • speeding up simulation: sub2ind is slow, do this instead.
  • Attempted merged approach, sometimes trying to move single molecules and sometimes moving all connected molecules. Groups still move slower than I think they should for realistic dynamics
  • wrote again to author of “Strings and Binders” paper to ask about algorithm again.
  • Contacted SD colleague and Berkeley colleague for suggestions on simulation.
  • Need to be able to break bonds rarely (seems to be a fundamental part of the algorithm at least).

MultiStain bead correction

  • no method aligns beads
  • Try brightfield / phase contrast images.



  • Need bench space and reagent space for Bogdan.
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