TBI Summer Course, Biocity, Turku, Finland

Dates: Aug. 7 - 10, 2012

course web site

Slides: Image Analysis in Cell and Developmental Biology (14Mb)

Click the link below and please find textbook pdf files.

• ImageJ Basics
  • We covered almost all of Chapter 1, and about a half of Chapter 2, 3, 4.

• ImageJ Macros
  • 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
  • Pincus Z, Theriot J a. Comparison of quantitative methods for cell-shape analysis. Journal of microscopy. 2007;227(Pt 2):140–56. Available at: http://www.ncbi.nlm.nih.gov/pubmed/20577976.

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

• Vaquerizas JM, Suyama R, Kind J, et al. Nuclear pore proteins nup153 and megator define transcriptionally active regions in the Drosophila genome. PLoS genetics. 2010;6(2):e1000846. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2820533&tool=pmcentrez&rendertype=abstract [Accessed December 31, 2010].

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

• Runz H, Miura K, Weiss M, Pepperkok R. Sterols regulate ER-export dynamics of secretory cargo protein ts-O45-G. The EMBO journal. 2006;25(13):2953–65. Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1500972&tool=pmcentrez&rendertype=abstract [Accessed February 7, 2012].

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: http://www.ncbi.nlm.nih.gov/pubmed/17210054.

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: http://www.ncbi.nlm.nih.gov/pubmed/8718670 [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: http://www.ncbi.nlm.nih.gov/pubmed/1478975.
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: http://www.ncbi.nlm.nih.gov/pubmed/9056409 [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: http://www.ncbi.nlm.nih.gov/pubmed/15189895.
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: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2941013&tool=pmcentrez&rendertype=abstract [Accessed August 7, 2012].

Slides below might be helpful as well

1. Molecular interactions investigated by quantitative colocalization measurements and number and brightness (N&B) analysis, by Peter Nagy (Dept. of Biophysics and Cell Biology, University of Debrecen)

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

• Object Tracking

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

• Correct 3D drift - Fiji
• The code is written in Jython (Python implemented in Java). This is a good example of how to do Jython scripting in Fiji.
  • code
• 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: http://www.ncbi.nlm.nih.gov/pubmed/21934862 [Accessed August 7, 2012].