Wednesday 07/02/14

10:00 am – 11:35 pm


  • Remove panel (c), add multiple examples of 405-cy5 BX-C spots for oligo-secondaries for previous panel (e)
  • Fix feducialDriftCorrection — github still preserves the lowercase name.
    • maybe best fix is to correct spelling (FiducialDriftCorrection)
  • write to Hazen Steve and Shu about fixed adaptive optics demo

STORM imaging sequential staining

  • finished staining L3C02, L3E05, L3D08toD12 and sequential stain prep BXC-P3 + F06-P1
  • imaging BXC-P3 part
  • some issues with stage. Had to use a screw to jammed into the stage from below to defeat the spring loaded catch that holds the stage insert in place (and prevents the stage z-piezo from moving up and down to correct z-drift).

simulation results with adaptiveLangevin







Python path errors

  • tried moving code out of site-packages directory. Get the following error:


This makes no sense to me, since it clearly found the polymerutils folder, since it found which sits inside the polymerutils folder (which is in site-packages, so it certainly should find it). But and getLinkingNumber is defined inside

Ah I see the problem: Python doesn’t distinguish the difference between folders and .py files and it is getting confused that there is a file in a folder called polymerutils\. I suspect it is looking for inside ...\site-packages\polymerutils\ rather than inside ...\site-packages\polymerutils\

Fixed this finally. Code now properly running from external folders.

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