Saturday 09/20/14

12:00 pm – 11:30 pm

multi-color epigenetic/structural boundaries

  • finalizing implementation / tests of the Bogdan’s Christofides TS algorithm for matlab
  • fixed some memory allocation issues, installed MinGW windows compiler in software to compile c code. Runs nicely. (Matlab may require reboot inbetween code compilation to load correct version after multiple system commands).
  • implemented linear bayesian separation plane computation. Works well at least when data are truly separated.
  • testing algorithms.
  • will need more evaluation tomorrow.
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Friday 09/19/14

10:00 am – 8:00 pm

Exploring new metric:

  • inspired by the dilate balls around each localization
  • fast / robust approach: 3D distance threshold to other points (threshold pdist matrix)
  • compute fraction of points from each channel colocalized with other channel (within threshold)
  • multiply this fraction by length in kb of the domain to give estimate of ‘kb entangled’

Working on chromatin figures

  • see git status

Discussing models

  • see protected notes.
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Wednesday 09/17/14

9:30 am – 10:30 pm


  • select some multicolor regions for a training set, send to BB
  • commenting on over interpretation of data in paper highlighted in the Crimson.

project 2

  • see notes
  • draft google presentation summary of results, share with team.

chromatin figures

  • working on internal black
  • working on cleaning up plotting code, plotting on linear axes.


  • recommendations for Sandy (vanO lab) about 3D super-resolution


  • attempting to image D08 (don’t have many cells)
  • dyes not switching off well (maybe didn’t add enough BME by accident?)
  • issues with microscope responsiveness
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Protected: project 2: analysis 09/17/14

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Tuesday 09/16/14

9:30 am – 1:00 am

AO demo

  • 9:30am – 12:00pm demo instruction with Rep
  • AO needs firewire connection to computer 2, can’t talk to the STORM3 computer
  • take calibration first with beads
  • 5:00pm – 6:00pm trying out sample

figure making

  • added errorbars and shaded confidence intervals for fits to figure 2.
  • functionalizing plotting commands (hopefully this makes the figure plotting code more readable and the long term figure making process faster)

chromatin data processing

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Monday 09/15/14

9:30 am — 4:50 pm, 9:30 pm – 1:15 am


  • lab meeting 10-12:15 pm, see notes
  • journal club 12:15 – 1:00 pm see notes
  • project 2 team meeting, 3:00 pm ? – ?

project 2 to do

  • see notes.

Chromatin analysis to do:

  • Density as a function of size
  • Volume as a function of size
  • standard error of mean ?
  • bootstrapping for uncertainty of the median.
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journal club 09/15/14

Guisheng: Nature, Auditory corollary discharge


  • different cortical regions interact strongly (e.g. motor cortex talks to other cortexes)
  • this is called “corollary discharge”.


  • auditory cortical excitatory connections are suppressed during movement.
  • apparent anticiaption of movement? — supression starts before and extends just past movement phase by ~1s on either side.
  • excitability by external stimuli is reduced during movement
  • inhibitory activity increases during movement (local effects)
  • stimulating axons from motor cortex that innervate auditory cortex results in repression of auditory cortex.
  • locomotion in absence of motor-cortex activity does not suppress auditory function.
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Protected: lab meeting 09/15/14

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Sunday 09/14/14

10:00 am – 11:59 pm


  • New Dave screwed up the sequence of events – moves before changing parameters
  • This has destroyed all my conventional images during STORM, and seriously bleached my dyes. — 750 region gets blasted with max UV and max 647
  • also forgot to change names, so my good conventional images are all overwritten in the runs prior to today.
  • hopefully the data is good enough I can do all the analysis straight from the STORM regions.

project 2

  • data analysis
  • data has issues. see post.
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Protected: project 2 update: 09/14/14

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