downloads:timeseriescolorcoder
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downloads:timeseriescolorcoder [2015/09/09 12:42] – [Reputations] kota | downloads:timeseriescolorcoder [2016/05/25 23:21] (current) – [Reputations] kota | ||
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+ | ~~NOTOC~~ | ||
+ | [{{ http:// | ||
+ | ====== 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:// | ||
+ | |||
+ | ==== 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): | ||
+ | * Del Castillo, U., Lu, W., Winding, M., Lakonishok, M., Gelfand, V.I., 2015. Pavarotti/ | ||
+ | * 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:// | ||
+ | * 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:// | ||
+ | * 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:// | ||
+ | * 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:// | ||
+ | * 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:// | ||
+ | * 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:// | ||
+ | * 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:// | ||
+ | * M. Basler and J. J. Mekalanos, 2012. Type 6 secretion dynamics within and between bacterial cells., Science 17; | ||
+ | ==== License ==== | ||
+ | Released under the GNU General Public License. | ||
+ | |||
+ | ==== Source ==== | ||
+ | |||
+ | [[https:// | ||
+ | ==== Requires === | ||
+ | ImageJ ver 1.34j or higher ([[http:// | ||
+ | |||
+ | ==== Installation ==== | ||
+ | |||
+ | It comes with ImageJ / Fiji, so you do not need to install it. | ||
+ | |||
+ | < | ||
+ | |||
+ | ==== Description ==== | ||
+ | |||
+ | Temporal changes in position of object will be color coded.\\ | ||
+ | For example, sequece such as | ||
+ | |||
+ | [{{ http:// | ||
+ | |||
+ | will be converted to color coded stack | ||
+ | |||
+ | [{{ http:// | ||
+ | |||
+ | Max intensity projection of this sequence yields | ||
+ | |||
+ | [{{ http:// | ||
+ | |||
+ | Coding table will also be created (check the option). | ||
+ | [{{ http:// | ||
+ | |||
+ | ==== 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.? |
downloads/timeseriescolorcoder.txt · Last modified: 2016/05/25 23:21 by kota