Category Archives: Microscopy

Protected: Confocal observations

Posted on February 6, 2011 by admin

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Protected: Confocal observations

Posted on February 3, 2011 by admin

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hb-gradient analysis

Posted on February 2, 2011 by admin

Analyzing hb-gradient: anlz_hb_gradient_data.m   (committed to Git). Circular field lines not appropriate (obviously).  Need to compute planes of separation instead. May be better to ensure original data has appropriate left-right planar orientation.  This will not only make segmentation easier, but … Continue reading →

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Improving dot z-segmentation

Posted on February 1, 2011 by admin

Improving z-dot segmentation double checking code: Turning mRNA counts into graphs.  With correcting for cell size variation gradient appears smoothly.  (I plot instead mRNA density per cell, and multiple by the mean cell volume to return to normalized total counts … Continue reading →

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Calibrating dot counting

Posted on January 31, 2011 by admin

Original DuplicateDots based on course graining and overlapping pixels not very precise results: Here green circles mark the red dots and yellow pluses mark the blue dots.  The two colors are confocal stacks separated by ~400nm.  As you can see … Continue reading →

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Protected: hb-transcription measuring

Posted on January 31, 2011 by admin

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DNA FISH

Posted on January 21, 2011 by admin

Bantignies and Cavalli publish new DNA FISH protocol (in Cell paper on Hox Gene kissing).  Recommend 15-25 kb for nicked translation: http://www.epigenome-noe.net/WWW/researchtools/protocol.php?protid=5.  Try using BACs as templates to start. Also recommend FISH Tag DNA Orange Kit (A555) for better signal. Try … Continue reading →

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high resolution imaging

Posted on January 15, 2011 by admin

More high resolution imaging of mRNA cytoplasmic transcripts. Depth indicated by color. To image: sna-y-full MP05, MP06, and MP10 (snail with and without shadows). To stain: hb-y-full dig, MP01, MP02, MP09

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Cell-cell variation in cytoplasmic mRNA

Posted on January 13, 2011 by admin

Using new Zeiss scope to quantify cell-cell variation in cytoplasmic mRNA. Note very few dots bleed through channels — most dots are red, blue, and green, rather than yellow, or cyan. High variation in Mg-alpha II LacZ expression, pretty low … Continue reading →

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