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EMBL BioImage Data Analysis



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Impressive and swift moderation @helenajambor !
About 3 hours, 31 mins ago by: Kota Miura (@cmci_)

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RT @LuisDVerde: Now available as a #ggplot2 geom thanks to @naupakaz
About 3 hours, 34 mins ago by: Kota Miura (@cmci_)

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RT @helenajambor: awesome, within 2 days .@naupakaz made a code publicly available for anyone wanting to make the half-and-half-plot FYI @…
About 3 hours, 35 mins ago by: Kota Miura (@cmci_)

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RT @dgaboriau: Thread on data visualisation: ggplots, boxplots and violin plots
About 9 hours, 12 mins ago by: Kota Miura (@cmci_)

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RT @christlet: SUSHI from Valentin Nāgerl lab allows super-resolution microscopy of neuronal morphology by STED imaging of extracellular sp…
About 12 hours, 22 mins ago by: Kota Miura (@cmci_)

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RT @christlet: Our work with @HenriquesLab and @MercerLab on SQUIRREL highlighted on the @CNRS website (in French, and we even found a pun!…
About 12 hours, 24 mins ago by: Kota Miura (@cmci_)
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CMCI weblog


Tried a new multichannel visualization tool: ImageSurfer.

I tried a 5D time series, which you could download using ImageJ File > Open Sample. Here are some impressions. I only tried with tiff-series and there was z-scale problem. Maybe this does not happen with other formats (leica or zeiss format).

  • limited to win32, no mac.
  • Importing tip:
    • For a image series with t-z-c ordered, select Timeseries - Slices - Color
  • setting for z-scaling is unknown. Isosurface rendering appears flat, ignoring scale setting of Tiff image.

Notes on MIPAV (tried with win32)

I tried MIPAV pretty long time a go (2005?). Compared to that time, MIPAV has evolved pretty much with stronger functionality in visualization. Many new algorithms fro filtering are added as well. Trials with test processing was mostly OK but some bugs, which are not ignorable. Rich and very advanced functions are implemented, but it tends to be that basic handling function is missing or hidden behind complex command bindings and not intuitive. “Vox” (volume of interest) concept is generally applied to most of the functions, and I think this point worth everyone interested to try out. We are trapped in 2D screen, while we want to access 3D - this is a common problem in all the software that deals with 3D datasets, and MIPAV is seeking for its solution.

MIPAV website:

checked followings:

  • is istallation light and easy?
  • what algorithms are available for filtering.
  • 3D rendering quality

Installation procedure quote from installation instruction

After installing the MIPAV from the jar file, be aware that for full functionality you will need the following installed into the Java Virtual Machine you will be using to execute MIPAV:

Java 1.5 (or later),
Java 3D 1.5.2 (or later),
JOGL 1.1.1 (or later), and
JMF 2.1.1e (or later).
Without all of these packages (remember that the $CLASSPATH must be set correctly), MIPAV may be only partially functional. Most affected by not installing Java 3D and JOGL are the 3D visualization functions.

To run mipav with a maximum heap size of 1000 megabytes use the following from a command line, where $mipav_install_directory is where you installed MIPAV to above:

cd $mipav_install_directory

java -Xmx1000M -cp .:lib/gsi-classes.jar:lib/jargon_v1.4.19.jar:
Release md5sum: 28e9a6f75ee168c1f282fa76284d5dca
Nightly md5sum: d6ae2449be40a418b74b162a3f94255c

=== comment on istallation === Not necessary to have above java modules for installation (but as instruction says, some functions will not do job. I will check later). For manually setting class path for visualization, google “set Classpath” or so.

Installing Plugins

LOCI plugin is available. For installation, also need to build the file and also setting class path manually.

–> according to LOCI instruciton, following steps must be taken (but maybe it works just by plugin → install plugins)

classpath of MIPAV: should edit the file mipav.lax
Add path to the plugin class below.

#   --------------
#   the Java classpath necessary to run this application
#   Can be separated by colons (Mac OS/Unix) or semicolons (Windows)

lax.class.path=.;help/mipav_help.jar;InsightToolkit/lib/InsightToolkit/InsightToolkit.jar;lib/JimiProClasses.jar;lib/jaxp/dom.jar;lib/jaxp/sax.jar;lib/jaxp/xalan.jar;lib/jaxp/xercesImpl.jar;lib/jaxp/xsltc.jar;lib/tar.jar;lib/jdom.jar;lib/iText-2.0.7.jar;lib/junit-4.4.jar;lib/WildMagic.jar;lib/jj2kpack.jar;lib/jhall.jar;lib/ACCESSION_client_VTool.jar;lib/axiom-api-1.2.4.jar;lib/axiom-dom-1.2.4.jar;lib/axiom-impl-1.2.4.jar;lib/axis2-kernel-1.2.jar;lib/bcprov-jdk15-136.jar;lib/commons-codec-1.3.jar;lib/commons-httpclient-3.0.1.jar;lib/commons-logging-1.1.1.jar;lib/jax-qname.jar;lib/jaxen-1.1-beta-10.jar;lib/neethi-2.0.1.jar;lib/rampart-core-ndar-1.2.jar;lib/rampart-policy-1.2.jar;lib/rampart-trust-1.2.jar;lib/wsdl4j-1.6.2.jar;lib/wss4j-1.5.2.jar;lib/wstx-asl-3.2.1.jar;lib/XmlSchema-1.3.1.jar;lib/xmlsec-1.4.0.jar;C:\\Documents and Settings\\Miura/mipav/plugins;C:\\Documents and Settings\\Miura/mipav/plugins/plugins.jar;lax.jar


Vey extensive and detailed documentation in the help file and vol.2 of the user guide (Volume2.pdf). This PDF is almost a text book. Worth checking through, since modern image processing algorithms are explained in details.
To see the list of implemented algorithm, check p51 - 62 of the pdf.


easy to convert 3D to 4D.
max projection over time is not possible
4D visualiazation: not clear.

ITK is wrapped (extensive documentation in the Help file )

c:\usr\local\bin\ITKAlgorithmsJava.dll c:\usr\local\bin\ITKBasicFiltersAJava.dll c:\usr\local\bin\ITKBasicFiltersBJava.dll c:\usr\local\bin\ITKCommonJava.dll c:\usr\local\bin\ITKCommonAJava.dll c:\usr\local\bin\ITKCommonBJava.dll c:\usr\local\bin\ITKIOJava.dll c:\usr\local\bin\ITKNumericsJava.dll c:\usr\local\bin\SwigRuntimeJava.dll c:\usr\local\bin\VXLNumericsJava.dll c:\usr\local\lib\InsightToolkit\InsightToolkit.jar This path of c:\usr\local is hard-coded into the build for the INSTALL project. You can relocate these files in a different folder and on a different machine, but you must keep the relative path locations between the ITK*Java.dll files and InsightToolkit.jar file the same. The reason for keeping the path relative is because the software in the InsightToolkit.jar file searches for the runtime DLLs using the relative path of “..\..\bin”.



Documentation is under development and could not really evaluate, but then:

  • tri-plane view of 4D sequence synchronized with the slider of the original stack.
  • surface rendering is not supporting 4D

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