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Timeline of @cmci_

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RT @WimJHH: EMBL Heidelberg workshop "Cryo-EM in Industry & Academia", 6-8 February 2019. Success stories, new technologies, industry chall…
About 5 hours, 9 mins ago by: Kota Miura (@cmci_)

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@f_levet @BertrandVernay I made it.
About 5 hours, 59 mins ago by: Kota Miura (@cmci_)

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RT @haesleinhuepf: One more session on #ImageJ short cuts: SHIFT+U opens the command tree. I didn't know this one. Thanks @BertrandVernay a…
About 6 hours, 11 mins ago by: Kota Miura (@cmci_)

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@ManuelTHERY @martinjones78 @NEUBIAS_COST Slowly Manu
About 15 hours, 53 mins ago by: Kota Miura (@cmci_)

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@laure_plantard I can’t track JY himself with Trackmate. Metaphysical contradiction.
About 17 hours, 45 mins ago by: Kota Miura (@cmci_)

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“2 chapters of my dissertation was only possible with Trackmate”
About 19 hours, 13 mins ago by: Kota Miura (@cmci_)
blogtng:blogtop
Algorithm FRAP Fiji ImageJ ImageJ Plugin ImageJ Plugin 3Dviewer Imaris Java Javascript Python R bias blog dokuwiki fiji google imagej java libraries matlab meetings neubias news papers python references software webadmin




CMCI weblog

Matlab Web Tutorials

I was asked about available web tutorials to learn Matlab from scratch: here is some links


Start

get to know Matlab

choose several from Matlab tutorials
http://www.mathworks.com/academia/student_center/tutorials/launchpad.html

or if you know a bit about command line interface

http://www.mit.edu/people/abbe/matlab/lec1.html http://www.mit.edu/people/abbe/matlab/lec2.html

should be quicker.

You could also go through a list of Matlab tutorials
http://www.duke.edu/~hpgavin/matlab.html

Image Processing

Matlab - R

very well documentation comparing Matlab and R.

http://www.math.umaine.edu/~hiebeler/comp/matlabR.html

Linked PDF contains huge number of functions in R equivalent to Matlab functions. Some useful discussions on difference between R and matlab could be found in

http://stackoverflow.com/questions/1738087/what-can-matlab-do-that-r-cannot-do

Writing Matlab code for ImarisXT

Getting Imaris object is pretty similar (see previous notes).

Found several links besides Bitplane site.

Aaron Christian Pontis Qu http://www.scs2.net/home/index.php?option=com_content&view=article&id=46:qu-for-matlab&catid=34:qu&Itemid=55&showall=1

Pretty much of communication with Imaris.

  • Sending 4D stack (successful with 8 z-slices, 46 timepoints tiff hyperstack)
  • Retrieving spots detected in Imaris back to matlab (I waited 5 minutes but currently not responding… finally, I got all the spots, none-filtered. It took time probably because I did not filter).

How to write Matlab Code for ImarisXT: a Short Tutorial http://sybil.ece.ucsb.edu/pages/imarisxt.html

this is a bit outdated.


I will further try doing something like

  • set parameters for spot detection from Matlab or Java
  • do spot analysis in Imaris using above setting
  • fetch the results of detected spots from Imaris to Matlab or Java
  • evaluate the quality. Change spot detecton parameter
  • do spot analysis again with updated parameter.
  • this looping goes on until certain satisfactory value is achieved, walk through parameter space.

For this, image stack itself stays in Imaris. Only parameter setting is exported from java/matlab to imaris, and analysis results are thrown back to matlab/java.

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Weblog Archive

blogtng/blogtop.txt · Last modified: 2016/05/24 05:46 (external edit)