Differences

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--- downloads:timeseriescolorcoder [2010/11/22 16:49] – kota
+++ downloads:timeseriescolorcoder [2016/05/25 23:21] (current) – [Reputations] kota
@@ Line 11: / Line 11: @@
 Tel: +49 6221 387 404
 ==== History ====
-  * 08-02-12??? created ver1 K_TimeRGBcolorcode.ijm\\
+  * 08-02-12 created ver.1 K_TimeRGBcolorcode.ijm
-  * 08-02-13??? stack slice range option added. ??? ???
+  * 08-02-13 stack slice range option added.
-    * time color code scale option added.? ???
+    * time color code scale option added.
-    * future probable addiition: none-linear assigning of gray intensity to color intensity??? ???
+    * future probable addiition: none-linear assigning of gray intensity to color intensity
     * -> but this is same as doing contrast enhancement before processing.
-==== Source ====
+  * 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 ====
-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...]**.
+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.\\ \\
+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 ====