documents:120807turku
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+ | ====== TBI Summer Course, Biocity, Turku, Finland ====== | ||
+ | Dates: Aug. 7 - 10, 2012 | ||
+ | |||
+ | [[http:// | ||
+ | ===== Lecture Slides ===== | ||
+ | |||
+ | [[http:// | ||
+ | |||
+ | ===== Practical Textbooks ===== | ||
+ | |||
+ | Click the link below and please find textbook pdf files. | ||
+ | |||
+ | * [[https:// | ||
+ | * We covered almost all of Chapter 1, and about a half of Chapter 2, 3, 4. | ||
+ | |||
+ | * [[https:// | ||
+ | * 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): | ||
+ | |||
+ | ===== 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; | ||
+ | |||
+ | ===== 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; | ||
+ | |||
+ | I did not talk about FRAP. In addition to Leong' | ||
+ | |||
+ | [[http:// | ||
+ | |||
+ | ===== Colocalization ===== | ||
+ | |||
+ | Recommended review: | ||
+ | |||
+ | - Bolte S, Cordelières FP. A guided tour into subcellular colocalization analysis in light microscopy. Journal of microscopy. 2006;224(Pt 3): | ||
+ | |||
+ | 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:// | ||
+ | - 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:// | ||
+ | - Fay FS, Taneja KL, Shenoy S, Lifshitz L, Singer RH. Quantitative digital analysis of diffuse and concentrated nuclear distributions of nascent transcripts, | ||
+ | - Costes SV, Daelemans D, Cho EH, et al. Automatic and quantitative measurement of protein-protein colocalization in live cells. Biophysical journal. 2004; | ||
+ | - Fletcher P a, Scriven DRL, Schulson MN, Moore EDW. Multi-image colocalization and its statistical significance. Biophysical journal. 2010; | ||
+ | |||
+ | Slides below might be helpful as well | ||
+ | - [[http:// | ||
+ | |||
+ | ===== Tracking ===== | ||
+ | |||
+ | List of available tracking softwares could be found in the link below. | ||
+ | * [[http:// | ||
+ | |||
+ | 3D drift correction I mentioned in the talk is in Fiji. | ||
+ | * [[http:// | ||
+ | * The code is written in Jython (Python implemented in Java). This is a good example of how to do Jython scripting in Fiji. | ||
+ | * [[http:// | ||
+ | * 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; | ||
+ | |||
+ | ===== ... other info will be added later. ===== | ||
+ |
documents/120807turku.txt · Last modified: 2016/05/24 12:46 by 127.0.0.1