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--- documents:120807turku [2012/08/15 09:55] – [Morphometry] kota
+++ documents:120807turku [2016/05/24 12:46] (current) – external edit 127.0.0.1
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+====== 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 =====
+D 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]]
+D 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. =====