Monthly Archives: February 2013

new SCM observations

Posted on February 5, 2013 by admin

It appears to me that AbdA and AbdB are more commonly ectopically expressed in replicating tissues of Scm mutants by shRNA knockdown. For example the over-replicating posterior and anterior regions found in some embryos also express these genes. (should have … Continue reading →

Posted in Summaries | Leave a comment

Protected: Meeting Notes

Posted on February 5, 2013 by admin

There is no excerpt because this is a protected post.

Posted in Research Planning | Tagged | Comments Off on Protected: Meeting Notes

Labeling antibodies with STORM dyes

Posted on February 5, 2013 by admin

Introduction Labeling antibodies with STORM dyes Secondary antibodies are labeled with a mixture of two amine-reactive dyes: an activator dye (Alexa Fluor 405, Cy2 or Cy3) and a reporter dye (Cy5, Alexa Fluor 647 or Cy5.5). After labeling, the number … Continue reading →

Posted in Summaries | Comments Off on Labeling antibodies with STORM dyes

Subbing Coverglass for STORM tissue-sections

Posted on February 5, 2013 by admin

Materials Thomas CoorsTek ceramic coverglass holders (2) 1M KOH (56.11 g KOH in 1000 ml H2O) 600 ml pyrex beakers (2) Gelatin (from bovine skin type B) Chromium potassium sulfate 95% EtOH (ethanol) Methods Place coverglass in ceramic holders: for … Continue reading →

Posted in Protocols | Comments Off on Subbing Coverglass for STORM tissue-sections

Monday 02/04/12

Posted on February 4, 2013 by admin

9:45 A — 6:30 P, 7:30P – 12:50 A Coding Implementing new method to compute z-calibration curves. See my saga of posts on the subject. Here’s the most recent post (with the least descriptive detail). Integrate new z-calibration computation method … Continue reading →

Posted in Summaries | Tagged , | Comments Off on Monday 02/04/12

z calibration part 3

Posted on February 4, 2013 by admin

Maximal alignment achieved through simulated annealing. Basically we have a whole bunch of short fragments of the longer, true z-curve, and we don’t know their z-offset displacement. So we jiggle them around and find the parts of them that match. … Continue reading →

Posted in General STORM | Tagged | Comments Off on z calibration part 3

Z-calibration part 2

Posted on February 4, 2013 by admin

Curves fit the following polynomial: $latex w_x=\sqrt{w_{x0} \sqrt{B_xX^4+A_xX^3+X^2+1}}$ where $latex X= (z-g_x)/(z_{rx})$ In general we will require $latex gx$ to be negative $latex gy$ to be positive. $latex Ax$ and $latex Bx$ are correction factors and should be small. See … Continue reading →

Posted in General STORM | Tagged , , | Comments Off on Z-calibration part 2

Z-calibration

Posted on February 3, 2013 by admin

Same set of molecules at a collection of different heights Challenges Stage tilted: all molecules in a given frame DO NOT have the same wx wy distortion. Stage started position uncertain — might not be mid-range. Stage z-drift during movie … Continue reading →

Posted in General STORM | Tagged | Comments Off on Z-calibration

Sunday 02/03/2012

Posted on February 3, 2013 by admin

11:00 A – 6:30P, 7:30P – 12:30 A STORM Finish O/N STORM run Take bead image z-calibration Take bead images for chromatic correction Copy data to Alistair8 Coding Fixed bugs in file export in STORMfinderBeta Generalize Z-calibration to work with … Continue reading →

Posted in Summaries | Tagged , | Comments Off on Sunday 02/03/2012

Coding Goals 02/02/13

Posted on February 3, 2013 by admin

Short Term Goals DaoSTORM Clean up calls for DaoSTORM in STORMfinder to use simplier DaoSTORM installation. (Complete 02/02/13) Test run DaoSTORM Merge all active projects in Matlab_STORM into Beta Move latest version of Insight3 and DaoSTORM in matlab-storm. (completed 02/02/13) … Continue reading →

Posted in General STORM | Tagged , | Comments Off on Coding Goals 02/02/13