![]() ![]() Having independent depth-cueing for surface (nearest-point) and interior (brightest-point) allows for more visualization possibilities. For both kinds, depth-cueing is turned off when set to zero (i.e.100% of intensity in back to 100% of intensity in front) and is on when set at 0 < n 100 (i.e.( 100 − n)% of intensity in back to 100% intensity in front). Interior Depth-Cueing works only on brightest-point projections. Surface Depth-Cueing works only on nearest-point projections and the nearest-point component of other projections with opacity turned on. Two kinds of depth-cueing are available: Surface Depth-Cueing and Interior Depth-Cueing. Generated regions (ROIs) are saved for each slice, so we can process the lungs from an image stack. Applies the magic wand with a specified threshold and at a specified point or points (X and Y values) on the images or slices from a stack. The trade-off for this increased realism is that data points shown in a depth-cued image no longer possess accurate densitometric values. Restarting ImageJ will add a 'Cell Outliner' command to the Plugins menu or a submenu of the Plugins menu. The depth-cueing parameters determine whether projected points originating near the viewer appear brighter, while points further away are dimmed linearly with distance. ROI Manager window will measure the region(. You can change the analysed line with the 'UP' and DOWN' key or by dragging the line with the mouse.Surface/Interior Depth-Cueing Depth cues can contribute to the three-dimensional quality of projection images by giving perspective to projected structures. Multiple regions can be selected by holding down the shift or control keys. 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. jar must be copied to the plugin folder or subfolder after restart ImageJ. 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. So, if we calculate the size of an RGB image, the total size will be counted. Tested with ImageJ 1.50i but should works on some older versions. Area statistics are calculated if there is no selection or if a subregion of the image has been selected using one of the first four tools in the tool bar. Others productions for ImageJ from the authors Measure Based on the selection type, calculates and displays either area statistics, line lengths and angles, or point coordinates. 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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