• CMCI ImageJ course Textbooks (2006-2012)

• EMBO Microinjection Course Reference List (2007.03.28)

• Practical: Analysis of Phototaxis Developmental Biology Predoc Course, Behavior Module (2009.11.25)

• Vector Field Analysis (10-03-03)

• Lecture Notes: Measuring movement of vesicles, virus and cells, EMBL Practical Course Advanced Microscopy (2010.03.11)

• Practical: Optimization of Analysis Strategy for Studying Microtubule Plolarity in Drosophila embryo, EMBL CBB Predoc Course (2010.10.21)

• Directionality Analysis, EMBO Cell Biology course (2011.11.00)

• ELMI meeting 2012, Leuven (2012.06.07)

• Biocity, Turku, Finland (2012.08.07)

• Natioanl Institute for Fusion Science, Gifu, Japan (in Japanese) (2012.09.25)

• Advanced Imaging Course (2012.10.05)

• EMBO High-Throughput Microscopy Course (2012.10.15-20)

• EMBL Cell Biology & Biophysics Course 2012 (2012.10.22-29)

• Small Number Biology Workshop (2013.07.28-08.10)

• |EMBL Cell Biology & Biophysics Course 2013(2013.10.21-27)

• |BioIT-EMBL Centres Joint Course 2014(2014.03.24-28)

• Small Number Biology Workshop (2014.07.28)

• FRAP analysis manual (updated 13-06-06)

• FRAP Internal Course (updated 10-04-26)

• FRAP analysis by fitting Gaussian Distribution (by Christian Tischer, 10-04-26)

• ImaegJ Macro Headless Limitations (2007)
• Interactively using ImageJ from Eclipse console - Installation (2010)
• Setting Up ImageJ Plugin Debugging Environment for Eclipse (2010)
• Using Fiji Jython interpreter in Eclipse (2012)
• Script Parameter CheatSheet (2019)
• Coding with PyimageJ in Container on VS Code (2022)

• Using ImageJ and R from Python simultaneously (2010)
• Using Matlab from Java (2010)

• ImageJ 3D Suite Javadoc

• Javascript & ImageJ,Fiji Cookbook
• Python (Jython) & Fiji Cookbook
• Python Image Processing Cookbook
• ImageJ Macro Fragments
• Java Tips
• ImageJ Scala coding setups
• R tricks
• Eclipse configuration
• OSX software
• CellCognition
• pygments ImageJ Macro Lexer
  • See example Latex file (example.tex) for the usage of minted package.

headless

• ImageJ with Cluster@EMBL (Short) - outdated
• ImageJ with Cluster@EMBL (details) - outdated
• Converting Leica LIF file series to Tiff stacks from command line
• Using Bioformats Command line Tools
• Passing stdout to ImageJ / Fiji

Python

• Compiling Spyder - outdated
• Building OpenCV with Python Binding - outdated

Server

• Using X Windows to use ImageJ and Fiji in server
• Silent ImageJ -X by Xvfp

Blog Entries

• ImageJ
• Matlab
• Imaris
• R
• Other Software

TEST

• test new server

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 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. 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. 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. 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. 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. 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. 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. 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. PubMed