ImageJ supports 8-bit, 16-bit and 32-bit (real) grayscale images and 8-bit and 32-bit color images. All operations will be performed on the active image. The active window has its title bar highlighted. ImageJ allows multiple images to be displayed on the screen at one time. It will not appear if the operation requires less then approximately one second. The progress bar, located to the right of the status bar, shows the progress of time-consuming operations. Memory available and percent memory used. The status bar, when the cursor is over an image, displays pixel coordinates and values.Īfter running a filter, it displays the elapsed time and processing rate in pixels/second.Ĭlick on the status by and it will display (as shown above) the ImageJ version, the Java version, memory in use, The tools and menus on the right side of the toolbar are created using Mouse over a tool and a description is displayed in the status bar. The toolbar contains tools for making selections, for zoomingĪnd scrolling images, and for changing the drawing color. The clipboard, edited, printed and saved. Histograms and plots are ordinary image windows that can be copied to Measurement results are displayed in the "Results" window. The "ImageJ" window contains a menu bar (at the top of the screen on the Mac), tool bar, status bar,Īnd a progress bar. To the public, so that the whole community benefits. The freedom to improve the program, and release your improvements.The freedom to redistribute copies so you can help your neighbor.The freedom to study how the program works, and change it to make it do what you wish.The freedom to run the program, for any purpose.An ImageJ user has the four essential freedoms defined by the Richard Stallman in 1986: ImageJ is public domain open source software. You can change the analysed line with the 'UP' and DOWN' key or by dragging the line with the mouse.Home | contents | previous | next Basic Concepts ImageJ is Free Software The highest peak between the two red lines is analysed to compute the sarcomere length displayed on the status bar. Red lines show the low and high frequency pass filters. Toolboxes for Analysis selection and Sarcomere length measurement.įFT spectrum (bottom right) of the grey profile (top right) of the highlighted line on the image. Toolbar providing icons to access SarConfoCal facilities. File is calibrated and ImageJ must set it correctly (time: 0.002 seconds, SL: 0.2773 microns)įor inquiries regarding feature requests, bug reports, or anything else related to the SarConfoCal macro, please email us. Channel 1: fluorescence and channel 2: transmission. Rat ventricular cardiomyocytes was loaded with fluo-4 AM. This file was recorded on an Olympus Fluoview 500. To test SarConfoCal, a linescan file with both fluorescence and transmission images is provided: Fluo4_VG05_linescan_calib0.28.tif. Eventually, you can visualize the FFT spectrum (button 3) N.B.: Most images from confocal microscopy can be imported with Bio-Formats, then spatial and temporal calibration should be correctly done. This should correspond to the pixel width. Verify the horizontal (spatial) calibration (button 2). This should correspond to the time of aqcuisition between two lines. Verify the vertical (temporal) calibration (button 1). For sarcomere length measurements, you need at least one channel with transmission image. Open in ImageJ a multi-channel image contening multiple lines from line-scanning confocal microscopy (x-scan horizontally, time vertically). 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 "SarConfoCal". Start ImageJ or restart it if already opened. Bioinformatics." Côme Pasqualin, François Gannier, Angele Yu, Claire O Malecot, Pierre Bredeloux, Véronique Maupoilĭownload SarConfoCal.ijm and copy it into the "ImageJ\macros\toolsets" folder. "SarConfoCal: simultaneous sarcomere length and cytoplasmic calcium measurements for laser scanning confocal microscopy images. SarConfoCal is used to analyse scanlines and multi-channel (fluorescence and transmission) from Laser Scanning Confocal Microscopy (LSCM) images of myocytes, then it plots the fluorescence signal and the sarcomere length of each line versus time. Tested with ImageJ 1.50i but should works on some older versions. Others productions for ImageJ from the authors SarConfoCal - Plugin for ImageJ to measure Fluorescence and Sarcomere Length from Laser Scanning Confocal Microscopy (LSCM) Images SarConfoCal - Simultaneous Fluorescence and Sarcomere Length Measurements from Laser Scanning Confocal Microscopy (LSCM) ImagesĬôme PASQUALIN - François GANNIER (gannier at univ-tours dot fr),
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