Wednesday, 01/01/2014

1:30p – 9:10p,
remotely, 12:30a – 1:15a


  • more Ph imaging Wt
  • New Year’s letter
  • website updates
  • Troubleshooting drift correction curves.
  • start working on dual-color ChromatinCropper

STORM for Ph project

  • The buffer has all gone, because I ran the thing too long.
  • Ph Wt imaging after about cell 6 buffer is dying out and image quality drops. Cells 6 to 12 lost
  • Mix up a new buffer, set up new imaging. Lets see if we can get away with fewer frames. 6 cells per buffer change is not looking so good.
  • Darn it I forgot to change the write directory, and hal has gone and overwritten all my data from last night!

STORM analysis

  • troubleshooting drift correction
  • some weird transpose somewhere needs to get fixed.
  • running resampled movie at sampling rate 1 to see if its something about my read and write dax.
  • Movie ran out of disk-space yesterday.
  • reran today, reran dot-finding analysis. For some reason InsightM comes up with a blank molecule list. Despite find lots of molecules.
  • Running in DaoSTORM for comparison (single round iteration, Z fit mode still). First, don’t seem to have to adjust overall intensity, for single round, maybe this is a new fix?)
  • Second observation, DaoSTORM is destroying insight in speed, with parameters chosen to find all the same dots. Like utterly many many fold faster.

seems indeed to be a transpose happening in my averager, haven’t figured out where yet though…

running no averaging vs. averaging seems to have little effect. Localization precision is pretty good, the dominant source of error seems to be erroneous bead movement.


Fixed bug in ReadDax subregion option that was transposing the image. ReadDax subregion feature could still use more testing, most of my test images are too symmetric.

coding matlab-storm

  • updated Tutorial for STORM-render

improved team approaches to git — discussion with Jeff

  • can pull completely separate repositories into eachother.
  • consequently should make my matlab-storm Beta its own repo under Alistair, it doesn’t need to have any of the same structure as matlab-storm

Zhuang-Lab master

  • These are stable release versions only. Probably only updated every few months
  • Updates should be tested first by non-developers (?)
  • remove user specific branches (not the right use of branches). Move these on to use specific repositories.


  • updated website ( at least a little bit
  • still need a new research page. Should organize papers into themes and one or two images each.
  • discovered Arjun Raj’s lab blog. Pretty good.
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