Tag Archives: coding

Tuesday 02/19/13

Posted on February 19, 2013 by admin

10:00A – 1:40P, 3:30P-12:10A Computer restart required for hotswap and to switch Alistair8 back to eSATA delete HB data from Alistair3b (now on Alistair3). disconnect Alistair3 future disk shuffling of earlier data might be better done on Tuck? remove Buffalo … Continue reading →

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improved cluster analysis

Posted on February 18, 2013 by admin

search radius cluster algorithm fastest implimentation is hist3 with binsize = search radius can easily require multiple molecules in the search radius by filtering: M=hist3([x,y],[Xmin:radius:Xmax,Ymin:radius:Ymax]); so if we want 15 nm search radius, just make 15nm steps M>3 require at … Continue reading →

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Sunday 02/17/13

Posted on February 17, 2013 by admin

STORM Finish O/N run of BXC + flank try2 (3D this time). Did not lose TIRF. Did not overfill drive or crash computer (4GB left on hard-drive, 400 written). Copying to new Alistair10. (will move to the new Alistair9 when … Continue reading →

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Saturday 02/16/13

Posted on February 16, 2013 by admin

10:30 A – 8:30P, 10:00P – 11:55P STORM Analysis DaoSTORM analysis still running on Fab7-A647 Pc-750 Read write steps from USB connected hard-drive very slow when this analysis is running. (I’m not sure how much slower the analysis goes to … Continue reading →

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Friday 02/15/13

Posted on February 15, 2013 by admin

9:30 A STORM Finish O/N run crashed hal when computer memory filled up. Need more external harddisks! Should do a test run on if we can save data on the fly from Hal over the network straight to Monet. Still … Continue reading →

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Thursday 02/14/13

Posted on February 14, 2013 by admin

9:20 A -7:00P, 9:00P – 10:30P STORM Finish O/N confocal More cells not in TIRF – sections not bleaching, even 647. Dropped TIRF angle to 14.2, now switching well, still good contrast. Might need to re-image this slide later today. … Continue reading →

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3D chromatic warp: Insight vs DaoSTORM

Posted on February 13, 2013 by admin

Results using 2013-13-02 Bead Data: Z-calibrations for this data set look pretty similar Comparing Chromatic warping DaoSTORM is actually getting a better fit and tighter warp, but not managing to get the same dynamic range in Z — only +/- … Continue reading →

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z-calibration: Insight vs DaoSTORM

Posted on February 13, 2013 by admin

with single iteration, Hazen 3D-DaoSTORM avoids splitting molecules more distant from frame A few notes on 3D-DaoSTORM First 4 iterations are computed with 4x the input threshold. So if using less than 4 iterations you want to quarter the threshold … Continue reading →

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chromatic warping: general formulation

Posted on February 11, 2013 by admin

Description of problem There are N different color channels which are imaged through different filters, and need to be mapped together to an accuracy greater than the resolution limit of the instrumentation / detection system (e.g. 10-20 nm for STORM, … Continue reading →

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Sunday 02/10/13

Posted on February 10, 2013 by admin

10:30 A – 11:35 P STORM Finish O/N STORM run of Fab7 running new chromatic 3D bead calibration (more positions, slightly narrower z-range) check out Hazen’s new Zee-calibrator — (looks like in progress viewer for data-fit curves). Doesn’t show molecules … Continue reading →

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