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====== SarcOptiM (High Frequency Online Sarcomere Length Measurement) ======

===== Introduction =====
SarcOptiM computes the spatial frequency of the striated pattern of a myocyte. It has been successfully tested on rat ventricular and atrial cardiomyocytes. Although not tested, it is expected to work on skeletal muscle fibers.\\ The analysis can be performed online on video capture inside ImageJ (e.g.: using the webcam plugin or HF_IDS_Cam plugin) or offline on a previously recorded video.
\\ In the online mode, the HF_IDS_Cam plugin with an IDS UI-1220LE camera allows high frequency online recording of sarcomere shortening (up to 1000 Hz) limited only by the frame rate of the camera.
\\ A complete description can be found in the above publication.

{{http://pccv.univ-tours.fr/ImageJ/SarcOptiM/img/Offline.png?800x550}}

===== Author =====
Francois Gannier (francois.gannier at univ-tours.fr)\\ Come Pasqualin (come.pasqualin at univ-tours.fr)

===== Publication =====
If you need to cite the plugin, please do so by citing the following paper: \\ 

"SarcOptiM for ImageJ: high-frequency online sarcomere length computing on stimulated cardiomyocytes"\\ Côme Pasqualin, François Gannier, Angele Yu, Claire O Malecot, Pierre Bredeloux, Véronique Maupoil.\\ American Journal of Physiology - Cell Physiology, Vol. 311, Num. 2, pages C277-C283. August 2016.\\ \\ Paper can be viewed here : [[http://ajpcell.physiology.org/content/311/2/C277.long]]

===== Download =====
The latest release of this plugin can be downloaded from here: [[http://pccv.univ-tours.fr/ImageJ/SarcOptiM/]]
\\ The source code can be found [[https://github.com/PCCV/SarcOptiM | on github]].

===== Installation =====
Download and unpack SarcOptiM.zip.
\\ Copy the SarcOptiM folder into the "ImageJ\plugins" folder.
\\ Copy the SarcOptiM.ijm file into the "ImageJ\macros\toolsets" folder.
\\ Start ImageJ or restart it if already opened.
\\ In the "More tools" menu (>>) of the toolbar, select "SarcOptiM". A new set of buttons should now be present on the right side of the toolbar, as shown in the top figure below. SarcOptiM is now ready to use. 

===== Licence =====
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation ([[http://www.gnu.org/licenses/gpl.txt]])\\ 
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.