10:00 am – 11:35 pm
Goals
- 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 openmmlib.py which sits inside the polymerutils folder (which is in site-packages, so it certainly should find it). But polymerutils.py and getLinkingNumber is defined inside openmmlib.py
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 polymerutils.py file in a folder called polymerutils\. I suspect it is looking for getLinkingNumber.py inside ...\site-packages\polymerutils\ rather than inside ...\site-packages\polymerutils\polymerutils.py.
Fixed this finally. Code now properly running from external folders.