Category Archives: Microscopy

Protected: ANT-C locus K27me3 by STORM try 1

Posted on August 15, 2012 by admin

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Protected: tissue specific Methylation state of the BX-C complex by STORM

Posted on August 15, 2012 by admin

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Code updates

Posted on August 3, 2012 by admin

updated with new data from snail mRNA counting (1x 4x and promoter studies) m Unsupervised_DotFinding.m m Unsupervised_DotFinding2.m m Unsupervised_DotFinding3.m + Unsupervised_DotFinding4.m + Unsupervised_DotFinding5.m + Unsupervised_DotFinding6.m + Unsupervised_DotFinding7.m + cyto2nucmap.m m fxn_nuc_seg.m + fxnclean_v2.m + fxnproject_color.m + imclean.m + imclean_1.mat + … Continue reading →

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issues with computing photon counts by exponential distributions

Posted on July 9, 2012 by admin

Fitting exponential distributions to molecule areas output from insight, multiplied by photon per count for gain 30  on STORM2 (.41 photons).       These data are all from Hazen’s 2D microtubules.  My 3D microtubules, Yari’s 2D sections, my 2D … Continue reading →

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last two weeks in images

Posted on July 5, 2012 by admin
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chromatic warp issues

Posted on June 6, 2012 by admin

warped image blurs out certain channels.  here 561 gets stretched along x. In the K27/K4 dataset 750 is dramatically stretched along x-y in a correlated fashion. Distortions get worse using higher order polynomial (e.g. 4th order).   Distortions are no … Continue reading →

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Protected: DNA-Oligo STORM try 1

Posted on March 24, 2012 by admin

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STORM3

Posted on March 19, 2012 by admin

STORM 3 setup notes 561 line: Com 8, up to 100 mW at detector when running at 300 mW at laser.  Controlled by AOTF 656 red line.  Power switch on tabel, modulated by AOTF.  up 100 mW at detector: mirrors … Continue reading →

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STORM run 03-14-12

Posted on March 14, 2012 by admin

sample Psc, K27 40 min etch, 330nm sections Laser Powers: 750=110mW, 647=110mW, 561 = 150mW, 488=150mW Start time = 7:25PM 561 very dense switching with 50% 405 power still at 35,000 frames.  stop it there. Occassional section has focal plane … Continue reading →

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Compare 2D and 3D spot finding results

Posted on March 2, 2012 by admin

2D in green, 3D in red (H3-647).   Z images are collapsed down into single plane.  It looks like brightness differences are substantial, better contrast total photons from 2D imaging (might have expected reverse, 3D apparently doesn’t compensate for photon … Continue reading →

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