====== TBI Summer Course, Biocity, Turku, Finland ======

Dates: Aug. 7 - 10, 2012

[[http://www.bioimaging.fi/2012/07/10/tbi-summer-course-on-light-microscopy-and-image-analysis-august-6-10th-2012/|course web site]]
===== Lecture Slides =====

[[http://cmci.embl.de/dls/20120807_ImageAnalysis_TurkuP.pdf|Slides: Image Analysis in Cell and Developmental Biology]] (14Mb)

===== Practical Textbooks =====

Click the link below and please find textbook pdf files. 

  * [[https://github.com/cmci/ij_textbook1|ImageJ Basics]]
    * We covered almost all of Chapter 1, and about a half of Chapter 2, 3, 4. 

  * [[https://github.com/cmci/ij_textbook2|ImageJ Macros]]
    * We covered basics, and then stopped at the dot animation macro (if-else).  


===== Morphometry =====

  * 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.

===== Distributions =====

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].

===== Kinetics, FRAP =====

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). 

[[http://cmci.embl.de/documents/100420frapinternal|Lecture Notes: FRAP internal course]]

===== Colocalization =====

Recommended review:

  - 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:

  - 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].
  - 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.
  - 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].
  - 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.
  - 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
  - [[http://embo2011.unideb.hu/sites/default/files/N&B+coloc_EMBO2011Debr_PeterNagy_0.pdf|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)

===== Tracking =====

List of available tracking softwares could be found in the link below. 
  * [[http://cmci.embl.de/mainpages/links2011#object_tracking mainpages:links2011 | Object Tracking]]

3D drift correction I mentioned in the talk is in Fiji. 
  * [[http://fiji.sc/wiki/index.php/Correct_3D_drift|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. 
    * [[http://fiji.sc/cgi-bin/gitweb.cgi?p=fiji.git;a=blob;f=plugins/Scripts/Plugins/Registration/Correct_3D_drift.py;hb=HEAD | 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]. 

===== ... other info will be added later. =====