Category Archives: Microscopy

troubleshooting hb stains

Purpose to start MERFISH experiments in Drosophila embryos Plan: use Biosearch probes to optimize RNA labeling using DNA probes currently using 20mers directly labeled. These aren’t working. Images from Shawn Little’s paper (Gregor lab) My RNA hb stains zoom out … Continue reading

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STORM2 dye and buffer testing

optimizing buffer conditions for deep 3D imaging of A647 and A750 labeled chromatin First buffer 750 and 647_storm_0001 – 0004 1/2x BME (new) 2 mM COT (new, reg strength) 350-380 mW 647 laser (2960 mA) 2100 mA of A750 1% … Continue reading

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Protected: project 2

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Code updates

updating other changes in directory. Old files may get restructured here soon into subdirectories. + .gitignore + Perry2011PNAS/read_planeT.m m Unsupervised_DotFinding.m + imclean.fig m imnucseg_pars0.mat m imnucseg_pars1.mat + imviewer.fig + imviewer_lsm.fig m imviewer_lsm.m m jacquestiffread.m updating other changes in directory. Old … Continue reading

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embryo sections

some sections lie nice and flat, others get substantial ripples. Is this knife compression? too large a section in x-y? (seems to correlate). Too thick a section? (seems also to be true in my experience).

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Code updates

minor tweak to TiffViewer m MatlabPhotoshop/TiffViewer.m minor tweak to TiffViewer split out assign dots to nuclei code from unsupervised dot finding script, so it can be called by other scripts. + AssignDots.m split out assign dots to nuclei code from … Continue reading

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Protected: SCM summary

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in situ update

[spreadsheet 0AjSqkxgziU1YdG90a29UaU5ua1FLUXZ5LTFmM1pMSlE 602 302 sheet=8]
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STORM4 alignment

Adding cylindrical mirror into beam path on STORM 4 and checking camera alignment and beam alignment Camera alignment Unscrew set-screw attaching camera port to microsocope body. ¬†The hex rench mounted on the back of the microscope fits this set screw. … Continue reading

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Protected: H3K27 in vivo structural dynamics

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