SarConfoCal - Simultaneous Fluorescence and Sarcomere Length Measurements from Laser Scanning Confocal Microscopy (LSCM) Images

Plugins and toolbars for ImageJ

Côme PASQUALIN - François GANNIER (gannier at univ-tours dot fr) University of Tours (France)

Date : 2016/06/27 first version

Please visit http://pccv.univ-tours.fr/ImageJ/SarConfoCal/ to download and for more information

Tested on ImageJ 1.50i (linux, Mac OS and Windows)

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

Open in ImageJ a multi-channel image contening multiple lines from line-scanning confocal microscopy (x-scan horizontally, time vertically). For sarcomere length measurements, you need at least one channel with transmission image.
Verify the vertical (temporal) calibration (button 1). This should correspond to the time of aqcuisition between two lines. Change it if needed.
Verify the horizontal (spatial) calibration (button 2). This should correspond to the pixel width. Change it if needed.

N.B.: Most images from confocal microscopy can be imported with Bio-Formats, then spatial and temporal calibration should be correctly done.