10:00 am – 11:30 pm
STORM
- imaging failed last night
- should have taken more alarm when the test image didn’t save
- parameters were default to
.647format which didn’t exist, resulting in save error. - computer auto-rebooted last night anyway
- Updating software
- updated imagewriters branched off new / stable storm2. Now have
.647and.750export options again. - tested update, pushed to my storm-control git branch as storm2_140815 branch
- could not reproduce jumpy behavior of steve for Hazen this morning, hopefully its done.
- updated windows on new computer to not allow automatic restart if users are logged in.
- Dave not issue not fixed (not so bad if first image is conventional. HB attributes this bug to JM. promises yet another version of Dave software coming soon anyway (eee hopefully this is better?).
- updated imagewriters branched off new / stable storm2. Now have
- setting up STORM imaging of chromatin-L4E1 (F10, first 100 kb)
- spots much brighter than the sample 3, which was supposed to have E1-E3 (first 300 kb of F10).
- Not really as bright as I’d expect though for 100 kb black region. Still not so sure the plate based method gives as good probes.
- we’ll see how things turn out in the proper analysis.
ChromatinCropper update
- relabel ‘channel1’ and ‘channel2’ — it’s already hardcoded to grab based on ‘647’ and ‘750’, so this ‘channel 1’ stuff is just confusing.
Ph Project
- checking images
- checking IQR values
- clarify which panels are which in Fig S1 (wouldn’t have been an issue if we labeled on the figures).
project 2
- validate and order primers
- seqs to Jeff to make secondaries for screen