11:00 am – 3:30 pm, 6:30 pm – 11:15 pm
STORM
- STORM2 froze during the night (click error provided an out of frame crash in python — built in check doesn’t catch it.
- debugged this with Bogdan, changed catch statement to check size of the object queried, not just the expected size of the image.
- restarted imaging of Ph-KD L2F03 with fresh buffer
- acquisition still looks good at movie 18. And rolling.
- need to take z-beads and chromatin beads tomorrow before Colenso starts.
Planning
- need to design and order new Green probes.
- need to analyze existing green data.
MERFISH
- figuring out parsing of new data schema
- trying to process L12 two-color data for analysis with Pipeline 5 or updated pipeline 1.
Nuclei live imaging
- took time lapse images of Hoechst stained nulcei (2 year+ expired DRAQ5 didn’t look that good at 1:10,000)
- took images of mock fix (replaced growth media with more growth media)
- took images of formaldhyde fixed cells
- took images of MeOH fixed cells (clearly shrunk)
- need to do some coding to analyze these.
- probably worth some manual playing with the Fiji tools too.
- some issues with Z-focus and x-y registration, largely sorted though.
Ph-Project
- check that numbers don’t change much upon down-sampling
Review
- reading article, drafting comments of first impressions
- very long methods section, reading imaging methods in detail