Monthly Archives: January 2011

Monday 01/31/11

Posted on January 31, 2011 by admin

9:40 A — 7:00P, 8:00P-11:40P Wrap-up confocal imaging: only 9 embryos finished by 10A.  Need faster scanning.  Most scans start and finish much too deep.  Need more optimization, try again tomorrow night. Hosting Ptashne (seminar 12p-1:30p, hosting lunch and issues … Continue reading →

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Calibrating dot counting

Posted on January 31, 2011 by admin

Original DuplicateDots based on course graining and overlapping pixels not very precise results: Here green circles mark the red dots and yellow pluses mark the blue dots.  The two colors are confocal stacks separated by ~400nm.  As you can see … Continue reading →

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Protected: hb-transcription measuring

Posted on January 31, 2011 by admin

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Sunday 01/30/11

Posted on January 30, 2011 by admin

12:00P – 7:00P, 9:00P – 11:50P Fixed github shadow enhancer repository (see post on the subject for details). Coding image processing of single mRNA FISH added code to im_singlemolecule.m/fig identify duplicate dots in adjacent scans based on position can adjust … Continue reading →

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Code maintenance

Posted on January 30, 2011 by admin

Purge binary data files from git repository to shrink repository size. $ bash git-delete-history.sh  binarydata.mat Uses script from David Underhill git-delete-history.sh Push updates to online repository to overwrite history (using force): $ git push origin master –force Ran on all … Continue reading →

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Conference Summary

Posted on January 30, 2011 by admin

Highlights Advanced Imaging Workshop: adaptive optics (J Kubby, Santa Cruz) subnanometer resolution imaging TIRF-free super resolution imaging (Alexandros Pertsin, Sloan) Gordon Conference: Stochastic physics in biology Stochastic transcription is hot live single protein counting.  Bursting in E coli transcription. (S … Continue reading →

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Saturday 01/29/11

Posted on January 29, 2011 by admin

10:00A — 1:30P Overnight imaging failed: offset incorrect, all images blank. Imaging lessons learned: organize multiple positions in a nearest-neighbor ordering to ensure that oil tracks appropriately with the lens.   Be sure to re-engage multiple tracks.  Be sure to … Continue reading →

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Friday 01/28/11

Posted on January 28, 2011 by admin

3:ooPM-4:00PM, 10:00P-12:45A Setting up overnight run on confocal, multiple positions snail-y and snail endogenous (and nuclei).   Quantify cell cell variation, variation in total mRNA, stability of yellow-snail-UTRs to endogenous snail, comparison of channels. Run fails due to offset issues. … Continue reading →

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Transcription discussions

Posted on January 27, 2011 by admin

Notes on Transcription modeling: need to be careful with discrete nature of Poisson cdf — incomplete gamma functions are not discrete, can’t throw away the floor function.  So you do need to wait at least until you have 1 bcd … Continue reading →

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Thursday 01/27/11

Posted on January 27, 2011 by admin

9:00 am – 12:30 pm Cellular and network evolution Discussion Leader: Zaida (Zan) Luthey-Schulten (University of Illinois) 9:00 am – 9:40 am Terry Hwa (UCSD) “Growth Transition, Persistence and Rapid Evolution of Antibiotic Resistance Provided by Growth-Mediated Intrinsic Feedback Loops” 9:40 … Continue reading →

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