Monthly Archives: March 2011

Image processing

Posted on March 14, 2011 by admin

Fixing automatic dot counting code: z-sections: small number of sections gives correct assignment.  Dots that extend into upper layers (line extends to the left) are not tracked, as they are marked when they first entered those layers.  Dots that extend … Continue reading →

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Sunday

Posted on March 13, 2011 by admin

3:15P –7:10P, 8:50P – 11:50P exploring effect of min dot size on mRNA counting. hunchback variation analysis — need better metric. collect phenotypic virgin hb rescues, clear rest. flip collection cages. O/N run on MP05s

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Saturday 03/12/11

Posted on March 12, 2011 by admin

8:50A – 11:30A, 12:30A – 7:00P, 8:00P-11:00P Finish ON confocal, at 9A exactly finished 9 embryos. letter trying to get help with publication fees. Sort male and female hb 3 rescues (1 male rescue, 400 + flies) Adjust gap shadow … Continue reading →

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Friday 03/11/11

Posted on March 11, 2011 by admin

8:50 A – 9:15 A, 10:15 A -11:15P Finish ON confocal, only 8 embryos imaged. Discussion with Mike and Mike about enhancer promoter models. Collect hb rescue virgins Flip collection cages, 11:00A, changed dot-finding threshold method to max dots. Troubleshooting … Continue reading →

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Thursday 03/10/11

Posted on March 10, 2011 by admin

10:35 A –7:05 P, 8:25 P – 12:00 A Finish description and figure for superposition model and alternatives (needs editing) Fly work: flip collection cages, flip MP08, collect hb rescue virgins separating nuclear mask creation and dot counting in im_singlemolecule. … Continue reading →

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Protected: snail patterning

Posted on March 9, 2011 by admin

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Wednesday 03/09/11

Posted on March 9, 2011 by admin

8:35 A — 9:15 A, 9:40 A — 2:00P, 2:40p-4:00P, 8:00P -10:00P Finish confocal scan.  only 28 images (of 36) taken.  Should have used scan-speed 5. Review Porcher results: hb[FB] = hb[15] (just use all fields and braket notation in … Continue reading →

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progress report

Posted on March 9, 2011 by admin

New Findings from Previous Goals: 1. Snail minus shadow rescues: Some embryos don’t gastrulate at all w/o shadow enhancer.  Preliminary results show some still do gastrulate.  Getting the numbers up next. 2. Stat sig. testing hb/kr/kni: see latest draft.  The … Continue reading →

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Tuesday 03/08/11

Posted on March 8, 2011 by admin

10:35 A –7:50 P, 8:30 — 12:00A Collect virgin hb rescues Still troubleshooting memory efficiency and speed of new 3d dotfinding code (see post). 1:00P flip new fly cages: MP08 snaD and cact/HbZ.  No time to fix. missed some embryos … Continue reading →

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optimizing image processing coding

Posted on March 8, 2011 by admin

Improving Efficiency and Speed of dot finding code.  (with upwards or 0.3 million dots segmented in a single stack, some substantial changes are necessary). Profiler on optimizing_dotfinding caught bug: needed to increase maxdots.  Now set automatically. Slow steps in CheckDotUpDown: … Continue reading →

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