Tag Archives: image processing

Friday 02/17/12

Posted on February 19, 2012 by admin

10:10 A — 6P, 8P-12:30P Finish O/N STORM run Analyze STORM data collect virgins working on alignment for STORM data.  Rigid alignment seems better for the moment. staining embryos, in situs day 3. New scheme for PcG and histone doubles: … Continue reading →

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Monday 02/13/12

Posted on February 13, 2012 by admin

10:00A -7P, 10P-12:20A Visiting postdoc talk (Bryan). 10A-1P Flip fly cage 1P. Some STORM stacks didn’t process in batchinsightm.  Some issues still in running code, tweaked code and re-running missing data sets: S45, S44ubx, Pc, S45_13i. Working on image registration … Continue reading →

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Tuesday 02/07/12

Posted on February 7, 2012 by admin

9:45 A — 8:00 P screwed up over-night run 561 channel for Ubx data — set delay to 15,000 and scan time 200 rather than scan to 15,000 frames. Analyzing STORM data from Sunday and Monday. batchinsightM not working right. … Continue reading →

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3D histone views

Posted on January 20, 2012 by admin

3D reassembly of microsection stack of STORM images of individual nuclei with pan-histone marker.  Some alignment issues still, but worth a comparison

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Friday 01/13/12

Posted on January 13, 2012 by admin

10:10 A -8:00P Start etching K4 Flip MP08 cage (10:40A) New MP08 cage cut eng-dig sections 3 – 4:30 cut new Ftz, eng labeled embryos 4:30 -6p, section’s of previously trimmed block do not hold together well. cut selection of … Continue reading →

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Sunday 12/25/11

Posted on December 25, 2011 by admin

writing new script for analyzing batches of snail data.  Using each slide as separate case called through the slides and switch command. fit sigmoids to right half of data compute coefficient of variation and mean expression for ‘on’ cells, defined … Continue reading →

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Friday 12-16-11

Posted on December 16, 2011 by admin

10:00A – 6:00P, 8:00P – 9:30P successful 3D pan-histone nuclear reconstructions bcd, ftz, H3 in situs post primary reaction, day 2.  incubating in primary antibody 2nd round with in situ primaries added to solution O/N at 4C. new in situs … Continue reading →

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Thursday 12-15-11

Posted on December 15, 2011 by admin

7:45 A – 8:30 P stopped O/N confocal run, only finished 6 embryos (11P recording start until 7:45A stop). hot washes for in situs (engrailed, ubx, antp, and MP08) split bcd, ftz, H3K4 embryos, start in situs with half of … Continue reading →

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mRNA counting control

Posted on June 6, 2011 by admin

  Double labeling, raw image (left), and competition labeling, raw image (right)                         Images are max-projects through the z-dimension.  hatches mark dotfinder located centroids.  Yellow stars mark mRNA transcripts found … Continue reading →

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