Tuesday 01/28/14

9:15a – 10:50a, 12:00p – 10:15p

Chromatin Project

Chromatin Analysis

Data Analysis

  • Continued analyzing D12 data from 10-26-13 up through image 26 (still plenty more dots to image).
  • F06 analyzed up to but not including image 0_2.

Developing analysis pipeline

  • updated CC to record locus name
  • mI is not computed correctly — this value changes depending on my zoom.
  • found origin of bug in mI computation: multiplied xy by pixelsize before subtracting centroid, so now the two distance measures were in different units. Will need to recompute for current data.
  • fixed bug in mI computation in ChromatinCropper.
  • running script to fix mI computation in all currently analyzed data.
  • if this looks better, let’s rerun it and record the new values into saved data structures.

Working on updated drift correction

  • changed method of calculating drift error
  • changed method of determining the guide bead
  • added
  • changed function name to function naming conventions (now called FeducialDriftCorrection.m). Added original function to a Depreciated folder — need to fade out function calls to this form feducialDriftCorrection.m

New cell staining

  • F03 + F04 (both P1 / A647)
  • G01 + G02 (both P1 / A647)


  • computing number of hamming codes with 4 ones for 32 hybes. (1240)
  • trick is to just use initial codewords with 4 or fewer ones before assigning parity bits
  • scaling up to 5 still yields memory errors. Because matlab won’t matrix multiply logicals.
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