====== Documents ======

===== Lecture Notes, Course Protocols =====
  * [[documents:IJcourses| CMCI ImageJ course Textbooks]] (2006-2012)

  * [[documents:MicroinjectReferenceList | EMBO Microinjection Course Reference List]] (2007.03.28)

  * [[documents:devbioBehaviorModule2009 | Practical: Analysis of Phototaxis]] Developmental Biology Predoc Course, Behavior Module (2009.11.25)  

  * [[documents:VectorField | Vector Field Analysis]] (10-03-03)

  * [[documents:100311AdvancedMicroscopy | Lecture Notes: Measuring movement of vesicles, virus and cells, EMBL Practical Course Advanced Microscopy]]  (2010.03.11)

  * [[documents:101021cbbpractical| Practical: Optimization of Analysis Strategy for Studying Microtubule Plolarity in Drosophila embryo, EMBL CBB Predoc Course]]  (2010.10.21)

  * [[documents:111100EMBOcourse| Directionality Analysis,  EMBO Cell Biology course]]  (2011.11.00)

  * [[documents:120607elmi|ELMI meeting 2012, Leuven]] (2012.06.07)

  * [[documents:120807turku|Biocity, Turku, Finland]] (2012.08.07)

  * [[documents:120925gifu|Natioanl Institute for Fusion Science, Gifu, Japan (in Japanese)]] (2012.09.25)
 
  * [[documents:121005AdvancedImg| Advanced Imaging Course]] (2012.10.05) 

  * [[documents:121019HTM|EMBO High-Throughput Microscopy Course]] (2012.10.15-20)

  * [[documents:121022Predoc|EMBL Cell Biology & Biophysics Course 2012]] (2012.10.22-29)

  * [[documents:130800SNB|Small Number Biology Workshop]] (2013.07.28-08.10)

  * [[documents:131021predoc||EMBL Cell Biology & Biophysics Course 2013]](2013.10.21-27)

  * [[documents:140326jointCourse||BioIT-EMBL Centres Joint Course 2014]](2014.03.24-28)

  * [[documents:140700SNB|Small Number Biology Workshop]] (2014.07.28)
===== FRAP Lectures=====
  * [[documents:Frapmanu | FRAP analysis manual (updated 13-06-06)]]

  * [[documents:100420FRAPinternal | FRAP Internal Course (updated 10-04-26)]]

  * [[:documents:100426frapgaussfit| FRAP analysis by fitting Gaussian Distribution (by Christian Tischer, 10-04-26)]]

===== CODING =====
  * [[documents:200720IJMacro_Headless| ImaegJ Macro Headless Limitations (2007)]]
  * [[documents:100825ImageJ_Jython_Eclipse| Interactively using ImageJ from Eclipse console - Installation (2010)]]
  * [[documents:100825ImageJ_Eclipse_debugging| Setting Up ImageJ Plugin Debugging Environment for Eclipse (2010)]]
  * [[documents:120618FijiJythonInEclipse| Using Fiji Jython interpreter in Eclipse (2012)]]
  * [[documents:190415IJMacro_ScriptParameters| Script Parameter CheatSheet (2019)]] 
  * [[documents:20221028Coding_PyimageJ_in_Container|Coding with PyimageJ in Container on VS Code (2022)]]

==== Bindings ====

  * [[documents:101105IJ_R_Jython|Using ImageJ and R from Python simultaneously (2010)]] 
  * [[documents:110524Java_Matlab|Using Matlab from Java (2010)]]

==== JAVADOCS ====
  * [[http://wiki.cmci.info/mcib3ddoc/| ImageJ 3D Suite Javadoc]]

==== Cookbooks & Tips====

  * [[documents:110822JSIP_Cooking:javascript_imagej_cookbook|Javascript & ImageJ,Fiji Cookbook]]
  * [[documents:120206PYIP_Cooking:python_imagej_cookbook|Python (Jython) & Fiji Cookbook]]
  * [[documents:110816PyIP_Cooking|Python Image Processing Cookbook]] 
  * [[documents:201021IJMacroFragments|ImageJ Macro Fragments]] 
  * [[documents:120329JavaTips|Java Tips]]
  * [[documents:121106ScalaSetUp|ImageJ Scala coding setups]]
  * [[documents:111012Rtricks|R tricks]]
  * [[documents:120904Eclipse|Eclipse configuration]]
  * [[documents:120905OSXinstallation|OSX software]]
  * [[documents:130327CellCognition|CellCognition]]
  * [[https://quantixed.org/2018/10/23/new-lexicon-how-to-add-a-custom-minted-lexer-in-overleaf/|pygments ImageJ Macro Lexer]]
    * [[https://github.com/miura/pygments_lexer_IJmacro|See example Latex file (example.tex) for the usage of minted package.]] 
===== Command Line =====
**headless**
  * [[documents:101103ImageJ_Cluster_Short| ImageJ with Cluster@EMBL (Short) - outdated]]
  * [[documents:100922ImageJ_Cluster| ImageJ with Cluster@EMBL (details) - outdated]]
  * [[documents:101029ImageJ_CUI_LIFconversion| Converting Leica LIF file series to Tiff stacks from command line]]
  * [[documents:101124LOCIBioformats_bftoolsTip| Using Bioformats Command line Tools]]
  * [[documents:20190416ijmacro_passingArguments| Passing stdout to ImageJ / Fiji]]

**Python** 

  * [[documents:110803CompileSpyder| Compiling Spyder  - outdated]]
  * [[documents:110816openCV| Building OpenCV with Python Binding  - outdated]] 

**Server**
  * [[documents:101126X11setup| Using X Windows to use ImageJ and Fiji in server ]]
  * [[documents:101213ImageJ_Silent| Silent ImageJ -X by Xvfp]]

**Blog Entries**
  * [[Documents:blogIJ|ImageJ]]
  * [[Documents:blogMatlab|Matlab]]
  * [[Documents:blogImaris|Imaris]]
  * [[Documents:blogR|R]]
  * [[Documents:blogSoftwareGeneral|Other Software]] 
  
**TEST**

  * [[documents:test201208| test new server]]
===== Publications =====
**Quantitative analysis of chromosome condensation in fission yeast. Molecular and cellular biology** Petrova, B., Dehler, S., Kruitwagen, T., Hériché, J.-K., Miura, K., & Haering, C. H. (2013). , 33(5), 984–98. doi:10.1128/MCB.01400-12
[[http://www.ncbi.nlm.nih.gov/pubmed/23263988|PubMed]]

**Nuclear pore proteins nup153 and megator define transcriptionally active regions in the Drosophila genome..** Vaquerizas JM, Suyama R, Kind J, Miura K, Luscombe NM, Akhtar A.  PLoS Genet. 2010 Feb 12;6(2):e1000846. [[http://www.ncbi.nlm.nih.gov/pubmed/20174442?dopt=Abstract |PubMed]]

**Functional analysis of the leading malaria vaccine candidate AMA-1 reveals an essential role for the cytoplasmic domain in the invasion process.** Treeck, M., Zacherl, S., Herrmann, S., Cabrera, A., Kono, M., Struck, N.S., Engelberg, K., Haase, S., Frischknecht, F., Miura, K., Spielmann, T. & Gilberger, T.W. PLoS Pathog. 2009 Mar;5(3):e1000322. Epub 2009 Mar 6. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=19283086&dopt=Abstract|PubMed]]

**Poleward transport of Eg5 by dynein-dynactin in Xenopus laevis egg extract spindles.** Uteng, M., Hentrich, C., Miura, K., Bieling, P. & Surrey, T. J Cell Biol. 2008 Aug 25;182(4):715-26. Epub 2008 Aug 18. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=18710923&dopt=Abstract|PubMed]]

**Birth and life of tissue macrophages and their migration in embryogenesis and inflammation in medaka.** Grabher, C., Cliffe, A., Miura, K., Pepperkok, R., Rorth, P. & Wittbrodt, J. J Leukoc Biol. 2007 Jan;81(1):263-71. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=17046968&dopt=Abstract|PubMed]]

**Dynamic organization of the actin cytoskeleton during meiosis and spore formation in budding yeast.** Taxis, C., Maeder, C., Reber, S., Rathfelder, N., Miura, K., Greger, K., Stelzer, E.H.K. & Knop, M. Traffic. 2006 Dec;7(12):1628-42. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=17118118&dopt=Abstract|PubMed]]

**Sterols regulate ER-export dynamics of secretory cargo protein ts-O45-G.** Runz, H., Miura, K., Weiss, M. & Pepperkok, R. EMBO J. 2006 Jul 12;25(13):2953-65. Epub 2006 Jun 22. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=16794576&dopt=Abstract|PubMed]]

**Live imaging of bidirectional traffic from the ERGIC.** Ben-Tekaya, H., Miura, K., Pepperkok, R. & Hauri, H.P. J Cell Sci 2005 Jan 15;118(Pt 2):357-67. Epub 2005 Jan 04. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=15632110&dopt=Abstract|PubMed]]

**Image quantification and analysis.** Miura, K. & Rietdorf, J. In Cell Imaging (Methods Express Series), 2005, ed. David Stephens, Scion Publishing Ltd.

**Tracking movement in cell biology.** Miura, K. Adv Biochem Eng Biotechnol 2005;95:267-95. [[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=16080272&dopt=Abstract|PubMed]]