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EMBL BioImage Data Analysis

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Timeline of @cmci_

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RT @martinjones78: Save the date! October 20th, @TheCrick Bioimage Analysis Symposium, registration opening in April #CBIAS https://t.co/6H
About 20 hours, 46 mins ago by: Kota Miura (@cmci_)

cmci_ avatar

A new data set in the NEUBAIS-@zenodo_org collection, contributed by @volker_b @NEUBIAS_COST https://t.co/FLx3q2hqM6
About 1 day, 1 hour ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @EuroBioImaging: Last chance to present your bioimaging analysis work at 4th NEUBIAS conference 👇 https://t.co/D4jfEVfWGo
About 4 days, 3 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @f_levet: You have until next monday to submit an abstract to the @NEUBIAS_COST Symposium. It's your last chance ! Go go go !
About 4 days, 4 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

Bioimage Analysis Lunch Heidelberg, Jan 2020 https://t.co/6FcCNzu1QJ
About 4 days, 4 hours ago by: Kota Miura (@cmci_)

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RT @Datascience__: DL@MBL: Deep Learning for Microscopy Image Analysis https://t.co/DT25zxxaRn #DeepLearning
About 5 days, 3 hours ago by: Kota Miura (@cmci_)
downloads:timeseriescolorcoder
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. 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.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. 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 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.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. 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. 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.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.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. Nature Physics *coverpage!
  • M. Basler and J. J. Mekalanos, 2012. Type 6 secretion dynamics within and between bacterial cells., Science 17;337(6096):815 pubmed

License

Released under the GNU General Public License.

Source

Requires

ImageJ ver 1.34j or higher (ImageJ, upgrade page).

Installation

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

Download K_TimeRGBcolorcode.ijm to a place where you can access easily. Install the macro by [Plugins→Macros→Install…].

Description

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

black and white dot

will be converted to color coded stack

color coded

Max intensity projection of this sequence yields

maxproj

Coding table will also be created (check the option).

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.


downloads/timeseriescolorcoder.txt · Last modified: 2016/05/25 16:21 by kota