When the best FFT is obtained, press "SPACE" to stop the "Online FFT Spectrum" analysis, be sure the image window is selected then choose the online or offline video analysis tool.ī) For full frame FFT analysis, two modes exist: SingleCell (AVI) or MultiCell (AVImc) N.B.: if the size of the line is changed by a factor 2 from a 2 n value (i.e.: 32/64/128/256/512.) you must stop and restart the "Online FFT Spectrum" analysis. The live display of the "Online FFT Spectrum" module should help you to find the best profile (i.e., a single peak as narrow and high as possible): while the FFT is displayed you can move the line or even change the angle (very useful also if the cell is moving during the experiment). Use the longest line possible: the ideal will be 256+ pixels while 64/128 is possible but give worse results. Trace a line along the cell long axis, this can be moved or resized later. Otherwise, use a time out equivalent to the video frequency (i.e., 1/frequency). On video capture, if the camera module is compatible (HF_IDS_Cam or webcam_Capture plugin v1.2) check "limit to Video Freq" in the different dialog boxes and enter a time out value COMPATIBLE with the video frequency, i.e., greater than 1/frequency. For temporal calibration, one needs to know the camera frequency. Spatial calibration is essential for the programme to search the sarcomere length within the limits of lengths given in the analysis parameters. For spatial calibration, this can easily be done by pressing CTRL+SHIFT+P or the "1µm" button on the toolbar and following the instructions of the dialog box, for example. ![]() Spatial and temporal calibrations of the video must be done. SarcOptiM from the "Plugins" menu alone shows some coding elements used in the script.ĭespite the fact that SarcOptiM can be used on entire image, using a simple line provides the best results. N.B.: To have access to the full functionalities of SarcOptiM, USE ONLY the toolbar. A new set of buttons should now be present on the right side of the toolbar, as shown in the top figure below. In the "More tools" menu (>) of the toolbar, select "SarcOptiM". ![]() Start ImageJ or restart it if already opened. "SarcOptiM for ImageJ: high frequency online sarcomere length computing on stimulated cardiomyocytes." Côme Pasqualin, François Gannier, Angele Yu, Claire O Malecot, Pierre Bredeloux, Véronique MaupoilĪmerican Journal of Physiology - Cell Physiology 2016,Ĭopy the SarcOptiM folder into the "ImageJ\plugins" folder.Ĭopy the SarcOptiM.ijm file into the "ImageJ\macros\toolsets" folder. 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. HF_IDS_Cam plugin) or offline on a previously recorded video. ![]() The analysis can be performed online on video capture inside ImageJ (e.g.: using the webcam plugin or Although not tested, it is expected to work on skeletal muscle fibers. It has been successfully tested on rat ventricular and atrial cardiomyocytes. SarcOptiM computes the spatial frequency of the striated pattern of a myocyte. Others productions for ImageJ from the authorsġ: add popup menu/a simple management for calibration/shortkey(type F1 on Online_FFT_spectrum window). SarCoptiM - High Frequency Sarcomere Length Measurement plugin for ImageJ SarcOptiM (High Frequency Online Sarcomere Length Measurement)Ĭôme PASQUALIN - François GANNIER (gannier at univ-tours dot fr)
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