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PhotoBend

839 bytes added, 21:55, 30 May 2019
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| publisher = American Chemical Society
| doi = 10.1021/acs.chemrev.5b00398
}}</ref> and an example of the bending process quantification in ref.<ref name="Cizhik2018>{{ cite journal| title = Quantification of photoinduced bending of dynamic molecular crystals: from macroscopic strain to kinetic constants and activation energies| author = Stanislav Chizhik, Anatoly Sidelnikov, Boris Zakharov, Panče Naumov and Elena Boldyreva| journal = Chemical Science| volume = 9| number = 8| pages= 2319-2335 | year = 2018| publisher = The Royal Society of Chemistry| doi = 10.1039/C7SC04863G}}</ref>).
[[Image:photobend_demo.gif|thumb|right|Animation of the photobend time lapse (~1500x playback speed)]]
There are two plugins in the collection providing two methods of crystal bending measurement: Bending_Crystal_Track and Laser_Spot_Track4. Both use the template matching technique based on OpenCV library to track the movement of specific targets in the series of time lapse images organized in the virtual stack. Direct usage of movies opened as image stacks is not supported currently (movies can be transformed in the image sequences with tools like ffmpeg. <span style="color:red"> UPDATE! - movies can be used directly with the Bending_Crystal_Track plugin! </span> Laser_Spot_Track4 stil requires a series of images). Timeline of the registered process is based on exif timestamps in the images or on the constant time step if the metadata are not available.
There is an ability to monitor a folder for additional images appearing in the time lapse series thus allowing live process registration. The plugins work with 8/16/32-bit greyscale or 24-bit RGB images. The matching mode can be chosen from the intensity-based or color-based for the RGB format (the later is useful for images having weak intensity contrast but possessing sufficient color gradients). Subpixel registration is available using local quadratic approximation of the matching measure.
* [[Update_Sites|{{bc|Help|Update...}}]]
* Click ''Manage update sites''
* Add and check new update site: Name=''PhotoBend'' , URL="http://sites.imagej.net/Anotherche/"
* Click ''Close''
* (You can skip this optional step by default) In the list of new jar files that are proposed to be installed from the update site, you can unchek files that do not need to be installed (for example, files not related to your operating system or processor architecture). To do this, change "Install / Update" to "Keep as is" for those files.
The dependencies are:
* javacv. Version 1.3.2 4 (opencv-version.jar file is copied into plugins folder to prevent automatic overwriting by Fiji updater)* joda-timexmpcore. Version 25.91.43* metadata-extractor. Version 2.911.0 == Citing ==We kindly ask you to cite ref.<ref name="Cizhik2018></ref> when publishing the results obtained using these plugins. Thank you for your support.1
== References ==
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