Tuesday 03/25/14

10:00a – 1:00a

Oligo Secondaries

  • Fixes for secondary figure
    • use the dots only rendering method
    • make dots only rendering method a standard plugin for matlab-storm (I rather like it)
    • wrote function StormHist.m added to QuickPlots of matlab-functions instead, not sure how general this will be.
    • downsizing the resolution of the STORM image of the simulation to simulate conventional image. This seems to work well, however the image ends up poorly centered (center is shifted to upper left as zoom get less). Can’t figure out why this is.
    • As nice as this with list2img and STORMcell2img, its actually a pretty simple function and maybe would be better to write from scratch as a stand alone call of hist3.
  • Sent current draft version back to Brian.
    • Should be good enough for writing, I don’t propose changing the storyline of the figure at all, just tweaking the actual images a bit.
    • I like the decompacted structure in this version better.


Ph projects

  • comments back from Kingston.
    • saved to disk. haven’t read yet.
  • Ajaz revising manuscript tactics with Nicole, will write later.



  • Forgot to do melt step on new multicolor stains last night! executed this morning at 9:30p

Data Processing

  • Launch analysis for L3C01 dataset
  • really should re-institute gain into bead images, bead image quality is marginal without it.
  • 2014-02-27_F04-6_F05-7
    • data is all unanalyzed. Processing now on Monet.
    • switching looks like crap.
    • 647 in particular everything is high-count low contrast and switching is horrible.
    • this is very likely the consequence of the mistaken preparation of 1M MEA in H2O instead of in acid
    • 750 data also looks poor, though not as bad relative to its norm as 647.


Data Organizing

  • Finished consolidating all multi-color data from ProBox1-7 onto ProBox8
  • To do: move multi-region single color data from ProBox8 onto ProBox7. This will help reduce confusion and make space for the multi-color data from RAID2 to go onto ProBox8.


Sample C02 imaged on prism2 (started last night)

  • O/N run on PRISM2 severe focus lock error at 8:45a (I wonder how good the images are from before then, this focus lock seems pretty happy to record off-set zero at a variety of different focal planes).
  • Finish imaging on PRISM2 at 11:00a.
  • several focus lock errors on PRISM2, need to check data for quality — might need to repeat this imaging session.

Sample C04 on prism2

  • Check Prism2 laser powers
    • 657 has 70 mW at back appeture (not bad, though this line is rather off peak spectrum)
    • 405 about 200 uW, set to ND filter position 3. Previous user has been blasting with 100% UV. This leaves my dyes permenantly on even at <1% AOTF laser power.
  • attempted to add auto gain. Not working. (note ^ does not exponentiate in python. Need to use **).
  • hopefully these beads are still usable (with a dynamic range of only 16!).

sample C03 on STORM2

  • laser powers 65 mW at backport with GUI set to 300 mW 647
  • attempted to branch storm2 and pull in DaxWriter-master from alistair storm-control. Resulting Hal configuration is non-functional.
  • switched back to old NewDaxWriter branch. This seems to still work fine.

A quick look at the C01 data


Project 2

Computer upgrades

  • Call CDW about getting windows 2012 quote with HHMI billing address — no reply, left message
  • academic license from NewEgg seems to quote in at considerably higher (600+ instead of 230). Not entirely clear it’s the right license either.


  • Finish reading Johnston and Desplan Science paper.
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