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documents:120807turku [2012/08/15 02:55]
kota [Morphometry]
documents:120807turku [2016/05/24 05:46] (current)
Line 1: Line 1:
 +====== 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. =====
 + 
documents/120807turku.txt · Last modified: 2016/05/24 05:46 (external edit)