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EMBL BioImage Data Analysis



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RT @SimonFlyvbjerg: Image analysis job opening in Wonderful Copenhagen
About 10 hours, 59 mins ago by: Kota Miura (@cmci_)

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RT @JekelyLab: Interested in connectomics? Join us in stunning Exeter! Postdoc opening to work on Platynereis serial EM data @UoE_Jobs @Uni…
About 10 hours, 59 mins ago by: Kota Miura (@cmci_)

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I like this kind of analysis - protein and organelle distributions
About 11 hours, 2 mins ago by: Kota Miura (@cmci_)

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Measuring radial intensity profile using custom IJ macro. Fig4b.
About 11 hours, 3 mins ago by: Kota Miura (@cmci_)

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RT @SfPRocur: One hashtag to follow for this kind of #sciart is #cellfie - different kinds of cells usually captured in a microscope. Look…
About 22 hours, 34 mins ago by: Kota Miura (@cmci_)

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RT @herrsaalfeld: Oh---look what just came out: @funkstille @srinituraga @cremi_challenge
About 23 hours, 53 mins ago by: Kota Miura (@cmci_)

TBI Summer Course, Biocity, Turku, Finland

Dates: Aug. 7 - 10, 2012

course web site

Lecture Slides

Practical Textbooks

Click the link below and please find textbook pdf files.

    • We covered almost all of Chapter 1, and about a half of Chapter 2, 3, 4.
    • We covered basics, and then stopped at the dot animation macro (if-else).


  • length
    • straight
    • curved
  • area
  • perimeter
  • circularity
  • The paper below is a good reference for knowing how to analyze shape in cell biology


3D measurement of nucleus foci positions: Method using distance map is written in the following article.

Kinetics, FRAP

The study of colesterol depletion effects on ER exit dynamics is in the following paper.

I did not talk about FRAP. In addition to Leong's lecture, you could follow the lecture notes below (if you are interested in modeling).

Lecture Notes: FRAP internal course


Recommended review:

  1. Bolte S, Cordelières FP. A guided tour into subcellular colocalization analysis in light microscopy. Journal of microscopy. 2006;224(Pt 3):213–32. Available at:

For those interested in Colocalization tests:

  1. Steensel B van, Binnendijk EP van, Hornsby CD, et al. Partial colocalization of glucocorticoid and mineralocorticoid receptors in discrete compartments in nuclei of rat hippocampus neurons. Journal of cell science. 1996;109 ( Pt 4:787–92. Available at: [Accessed August 7, 2012].
  2. Manders EM, Stap J, Brakenhoff GJ, Driel R van, Aten J a. Dynamics of three-dimensional replication patterns during the S-phase, analysed by double labelling of DNA and confocal microscopy. Journal of cell science. 1992;103 ( Pt 3:857–62. Available at:
  3. Fay FS, Taneja KL, Shenoy S, Lifshitz L, Singer RH. Quantitative digital analysis of diffuse and concentrated nuclear distributions of nascent transcripts, SC35 and poly(A). Experimental cell research. 1997;231(1):27–37. Available at: [Accessed August 7, 2012].
  4. Costes SV, Daelemans D, Cho EH, et al. Automatic and quantitative measurement of protein-protein colocalization in live cells. Biophysical journal. 2004;86(6):3993–4003. Available at:
  5. Fletcher P a, Scriven DRL, Schulson MN, Moore EDW. Multi-image colocalization and its statistical significance. Biophysical journal. 2010;99(6):1996–2005. Available at: [Accessed August 7, 2012].

Slides below might be helpful as well


List of available tracking softwares could be found in the link below.

3D drift correction I mentioned in the talk is in Fiji.

  • The code is written in Jython (Python implemented in Java). This is a good example of how to do Jython scripting in Fiji.
  • The algorithm of this plugin is similar to what is described in this paper
    • Mlodzianoski MJ, Schreiner JM, Callahan SP, et al. Sample drift correction in 3D fluorescence photoactivation localization microscopy. Optics express. 2011;19(16):15009–19. Available at: [Accessed August 7, 2012].

... other info will be added later.

documents/120807turku.txt · Last modified: 2016/05/24 05:46 (external edit)