~~NOTOC~~
[{{ http://cmci.embl.de/weblog/uploaded_images/timecolorcoder-732700.jpg?200| Time Series Color Coder}}]
====== Time Series Color Coder ======
Color coding traces by time.

==== Author ====
Kota Miura\\ 
Centre for Molecular and Cellualr Imaging (CMCI)\\ 
EMBL Heidelberg\\ 
miura at embl dot de\\ 
Tel: +49 6221 387 404 
==== History ====
  * 08-02-12 created ver.1 K_TimeRGBcolorcode.ijm 
  * 08-02-13 stack slice range option added.
    * time color code scale option added.
    * future probable addiition: none-linear assigning of gray intensity to color intensity
    * -> but this is same as doing contrast enhancement before processing. 
  * 10-12-06 ... is now part of Fiji. [[http://pacific.mpi-cbg.de/wiki/index.php/Temporal-Color_Code | See details in the Fiji web site.]]

==== Reputations ====

  * 1. Schulze N, Graessl M, Blancke Soares A, et al. FHOD1 regulates stress fiber organization by controlling the dynamics of transverse arcs and dorsal fibers. J. Cell Sci. 2014;127(Pt 7):1379–93.[[http://www.ncbi.nlm.nih.gov/pubmed/24481812|PubMed]].
  * Del Castillo, U., Lu, W., Winding, M., Lakonishok, M., Gelfand, V.I., 2015. Pavarotti/MKLP1 regulates microtubule sliding and neurite outgrowth in Drosophila neurons. Curr. Biol. 25, 200–5. [[http://www.ncbi.nlm.nih.gov/pubmed/25557664|PubMed]]
  * Tobias Dürig, Magnus T Gudmundsson and Pierfrancesco Dellino, Reconstruction of the geometry of volcanic vents by trajectory tracking of fast ejecta - the case of the Eyjafjallajökull 2010 eruption (Iceland), Earth, Planets and Space 2015, 67:64 [[http://www.earth-planets-space.com/content/67/1/64|Earth, Planets and Space]]
  * Lu, W., Lakonishok, M., Gelfand, V.I., 2015. Kinesin-1-powered microtubule sliding initiates axonal regeneration in Drosophila cultured neurons. Mol. Biol. Cell 26, 1296–307.[[http://www.ncbi.nlm.nih.gov/pubmed/25657321|PubMed]]
  * Brown, A.K., Hunt, S.D., Stephens, D.J., 2014. Opposing microtubule motors control motility, morphology and cargo segregation during ER-to-Golgi transport. Biol. Open. [[http://www.ncbi.nlm.nih.gov/pubmed/24705013|PubMed]]
  * Akamatsu, M., Berro, J., Pu, K.-M., Tebbs, I.R., Pollard, T.D., 2014. Cytokinetic nodes in fission yeast arise from two distinct types of nodes that merge during interphase. J. Cell Biol. 204, 977–88. [[http://www.ncbi.nlm.nih.gov/pubmed/24637325 | PubMed]]
  * Galic, M., Tsai, F.-C., Collins, S.R., Matis, M., Bandara, S., Meyer, T., 2014. Dynamic recruitment of the curvature-sensitive protein ArhGAP44 to nanoscale membrane deformations limits exploratory filopodia initiation in neurons. Elife 3, e03116.[[http://www.ncbi.nlm.nih.gov/pubmed/25498153|PubMed]]
  * Robert, A., Herrmann, H., Davidson, M.W., Gelfand, V.I., 2014. Microtubule-dependent transport of vimentin filament precursors is regulated by actin and by the concerted action of Rho- and p21-activated kinases. FASEB J. 28, 2879–90.[[http://www.ncbi.nlm.nih.gov/pubmed/24652946|PubMed]]
  * Alvarado, J., Sheinman, M., Sharma, A., MacKintosh, F.C., Koenderink, G.H., 2013. Molecular motors robustly drive active gels to a critically connected state. Nat. Phys. 9, 591–597. [[http://www.nature.com/nphys/journal/v9/n9/full/nphys2715.html|Nature Physics]] ***coverpage!**
  * M. Basler and J. J. Mekalanos, 2012. Type 6 secretion dynamics within and between bacterial cells., Science 17;337(6096):815 [[http://www.ncbi.nlm.nih.gov/pubmed/22767897|pubmed]]
==== License ====
Released under the GNU General Public License. 

==== Source ====

[[https://github.com/fiji/fiji/blob/master/plugins/Scripts/Image/Hyperstacks/Temporal-Color_Code.ijm|GitHub]]
==== Requires ===
ImageJ ver 1.34j or higher ([[http://rsb.info.nih.gov/ij/upgrade/|ImageJ, upgrade page]]). 

==== Installation ====

It comes with ImageJ / Fiji, so you do not need to install it. 

<del>Download [[http://cmci.embl.de/dls/K_TimeRGBcolorcode.ijm|K_TimeRGBcolorcode.ijm]] to a place where you can access easily. Install the macro by **[Plugins->Macros->Install...]**. </del>

==== Description ====

Temporal changes in position of object will be color coded.\\
For example, sequece such as 

[{{ http://cmci.embl.de/dls/colorcoder/dotanimation.gif |black and white dot}}] 

will be converted to color coded stack 

[{{ http://cmci.embl.de/dls/colorcoder/colored.gif |color coded}}]

Max intensity projection of this sequence yields  

[{{ http://cmci.embl.de/dls/colorcoder/MAX_colored.jpg |maxproj}}]

Coding table will also be created (check the option). 
[{{ http://cmci.embl.de/dls/colorcoder/colortimescale.jpg | timescale color coded}}]

==== Work Flow ====

1. Open a stack (8 bit or 16 bit)\\ 
2. Run the macro\\ 
3. In the dialog choose one of the LUT for time coding.?Select frame range (default is full). Check if you want to have color scale bar.\\ \\ \\