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Tagsanalysis cell culture cell labeling chromatin cloning coding communication confocal data analysis embryo collection embryo labeling figures fly work genomics hb image analysis image processing images in situs Library2 literature making antibodies matlab-storm meetings modeling MP12 mRNA counting Ph planning presentation probe making project 2 project2 result results sectioning section staining shadow enhancers sna snail staining STORM STORM analysis troubleshooting writing
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10:00 am – 11:30 pm
- see post
- need to fix multichannel drift correction in new version of ChromatinCropper
10:50 am – 11:00 pm
- video editing for XZ?
- Finish revisions to BW Essay. Send to XZ.
- Start working on review
- project 2, design next 2 set of experiments
- reading and editing paper.
- finished reading and making notes.
- still need to assemble notes into a coherent review essay.
Discussion with Bogdan
- will share data on Cajal
- Stark’s totally awesome genome scale enhancer screen, finally in print.
9:30 am – 10:30 pm
- some further questions
- can we find a fundamental unit of yellow that is (more) self-interacting if we go to smaller internal sizes?
- working on figure layout
- project 2 meeting
- ice bucket challenge for Xiaowei
- discussing project goals with Jeff
- interesting article on chromatin state dynamics in blood development
9:00 am – 11:30 pm
- working on figures
- trying to lay out story — let’s formulate this as a presentation first.
- I think the volume/pixel scaling and the Rg scaling actually provide some different information. Moreover they lend themselves to emphasize different parts of the data
- the ‘getting denser’ is most obvious from the ‘volume’ data
- shape changes that don’t affect density could still cause Rg to decrease (e.g. becoming more symmetrical).
- these are also different forms of data in the pixel vs vector representations
- Rg data makes a better statistic for comparing against other models (like the random walk).
- working on data analysis
- growing really slowly :(.
- comment on Raj lab blog discussion “is academia broken or just really hard“
9:30 am – 11:30 pm
- working on figures to compare internal vs intact blue scaling (see post).
- analyzing new data (see post)
- poster session in Naito
- new CRISPR/Cas9 transgenic targeted insertion toolkit being developed by Perrimon lab. Looks very cool.
10:00 am – 11:30 pm
- some revisions to BWF proposal in response to vague comments from XZ.
- finalize and submit reviewer comments for recent manuscript (review due Wed)
- Re-aligning STORM2
- re-aligned backport optics
- 561 and 647 beams are no longer aligned prior to backport optics (too much tweaking of the mirrors in front of the lasers…)
- Tried to balance brightness and flatten field. Upper portion of 647 channel is still a bit dim.
- Improved alignment of quadview somewhat (less of the field of view is cut off. These shutters and lens controllers are getting pretty sticky…
Chromatin Spot Data collection
- multiple spots for G10 spots from chrX.
- Maybe 2 months in culture has been a bit too long for these guys.
- Started new cells from frozen stock. Seem to be growing alright.
- Analyzing black domains