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EMBL BioImage Data Analysis



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RT @biomicugm: Topics: Biostatistics, computational evolutionary biology, computational genomics and proteomics, graph models, image analys…
About 4 days, 16 hours ago by: Kota Miura (@cmci_)

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RT @JustinMCrocker: We are looking for an interdisciplinary EIPOD postdoc to join our group @EMBL! Potential projects with @Eileen_Furlong,…
About 4 days, 16 hours ago by: Kota Miura (@cmci_)

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RT @BioImagingUK: This maybe of interest to the @NEUBIAS_COST @openmicroscopy communities #imageAnalysis #imagingScientist
About 4 days, 16 hours ago by: Kota Miura (@cmci_)

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RT @BioImagingUK: Software developer position on large image data analysis - working closely with the lab of @bayraktar_lab @sangerinstitut…
About 1 week, 2 days ago by: Kota Miura (@cmci_)

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RT @AssafZaritsky: Modeling the interplay of lamellipodial motion and the intercellular actomyosin cable during epithelial wound healing h…
About 1 week, 2 days ago by: Kota Miura (@cmci_)

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RT @jytinevez: @florianjug says be careful when using #CARE for intensity based quantification; CARE restoration is like a non linear trans…
About 1 week, 4 days ago by: Kota Miura (@cmci_)
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


get to know Matlab

choose several from Matlab tutorials

or if you know a bit about command line interface

should be quicker.

You could also go through a list of Matlab tutorials

Image Processing

Matlab - R

very well documentation comparing Matlab and R.

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

Writing Matlab code for ImarisXT

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

Found several links besides Bitplane site.

Aaron Christian Pontis Qu

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

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)