Checking out 08/26/16

Last day!

It’s my last day in the Zhuang lab and this my last notebook post.

For the last 6 months, I’ve predominantly shifted to using an IPython based notebook hosted on the ZhuangLab github website ( Bogdan and I have shared notebooks there and it is a private repository. That notebook I also downloaded today for my records.

STORM6 is built and collecting data.

We took some single molecule data yesterday for quantitative comparison. It still needs rigorous analysis but looks reasonable. The main difference on imaging on STORM3 is the TIRF is better, and helps substantially with foreground-to-background issues.

The notch filter to reduce scatter helps a tiny bit, the beam clean-up filter doesn’t really help. Changing to the STORM3 oil also doesn’t make a visible difference but has a slight quantitative effect to improve contrast. Both were HF oil (EM on STORM6 vs. Cargylle from STORM3). Might try some other oils, but the HF oil doesn’t seem to be making any problems for the STORM3 contrast.

I think it will be improved by the addition of a beam shaper (ordered). It is difficult to get the whole field to go into TIRF evenly, some more research on objective type TIRF might help here, but there are probably limits to beam size for objective type TIRF, especially in using non-TIRF objectives (though the TIRF ones have more chromatic or flatfield aberation not being “Plan” and are twice the price).


  • clean out freezers
  • download and save notebooks to disk for XZ
  • organize data drives for XZ
  • clean desk and drawers
  • ship primers, probes and libraries necessary to assist BB with current DNA imaging project.
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