Tag Archives: STORM analysis

Saturday 03/29/14

Posted on March 29, 2014 by admin

10:15a – 12:15a Multi-color data analysis Analyzing chromatic bead data from 2014-02-27 and 02-28 Analyzing drift bead data from 2014-02-27 / 28 should write a little script to auto launch this stuff? 2014-02-28 F06F05 dataset, Image 25 and on, Conventional … Continue reading →

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Monday 12/16/13

Posted on December 16, 2013 by admin

9:50a – 1:00a Group meeting 10a – 2p see notes Probe making cy7 dye from Lumipore arrived A750 labeled IDT primers arrived first test gel — try old gel of Bogdan’s (11/18). Ran smeary and fast, primers ran off the … Continue reading →

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Saturday 12/14/13

Posted on December 14, 2013 by admin

11:15a – 2:30p, 6:00p – 11:45p Coding matlab-storm test installation: created new ZhuangLab account Install for Guipeng. DaoSTORM objects to spaces in pathname. adding double quotes ” does not fix. library Prep New function (in Genomics Functions toolbox) function Seq … Continue reading →

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Friday 12/13/13

Posted on December 13, 2013 by admin

10:45a – 12:15a Notebook backed up notebook updated wordpress Z-calibration cross correlation doesn’t improve curve alignment visibly — curves are fundamentally a bit different no spatial structure evident Ph Project reviewing simulation results saved as simulationName_2.eps to file Test new … Continue reading →

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Thursday 12/05/13

Posted on December 5, 2013 by admin

9:30a – 12:20a Goals Restart analysis for project 2 Probe making: check PCRs, continue if good, restart if not. launch STORM analysis for last few days of imaging project 2 see notes. Chromatin Project Probe Making Test PCRs Clean, reorganize, … Continue reading →

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Monday 12/02/13

Posted on December 2, 2013 by admin

9:00a – 12:20a Goals work on data analysis / slides for meeting with Ting tomorrow new round of yellow chromatin RNA DNA double stains. Include attempt restain E10rna. Still needs RNase. 3D z-calibration [POSTPONED] Start statistical analysis of Blue Polymer … Continue reading →

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Saturday 11/23/13

Posted on November 23, 2013 by admin

10:00a – 11:00p STORM2 Helping Guipeng and Ruobo get set up on STORM2. Cell staining prepping cells for hybridizaton. last row (4 coverslips) forgot to add last rinse of PBS. Cells dried out. Coverslips tossed. cells into formamide, ready for … Continue reading →

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Wednesday 11/20/13

Posted on November 20, 2013 by admin

10:15a – 10:00p Goals prepare slides for chat with Levine Reply to SW Genome Analysis Mi Seq analysis of off target hybridization sequence bias New strategy: Generate new fasta file with the entry ID number as the first 5 digits … Continue reading →

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Thursday 10/07/13

Posted on November 7, 2013 by admin

9:25a – 11:50p Probe Making very poor probe incorporation. Maybe the lower concentration of Maxima? Try to run RT again tomorrow to compare. attempted DCC of probes to remove excess primer using short probes 1-4. Extremely low yield (20 ng/uL … Continue reading →

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Saturday 11/02/13

Posted on November 2, 2013 by admin

9:00a – 12:00p remotely. 12:00p – 12:00a Goals Coding Add to ChromatinCropper export labeled overview fig, object centroid and bounding box in original coordinates (for computation of distance to lamina) direct measure of distance to lamina New functionalities for ChromatinCropper … Continue reading →

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