Image Analysis 1 1- Introduction to image analysis software “ImageJ” -development history -ImageJ vs. Fiji -installation -ImageJ website -sample images -tour of software environment 2- Basic image analysis using ImageJ: -opening/saving a file -file size vs. bit-depth and image-resolution -calibration -histograms, “live updates” -contrast, brightness, saturation -measurement: linear profiles, statistical information -Region of Interest (ROI) and local measurements/manipulations -image calculations 1
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Image Analysis 1
1- Introduction to image analysis software “ImageJ”
-development history
-ImageJ vs. Fiji
-installation
-ImageJ website
-sample images
-tour of software environment
2- Basic image analysis using ImageJ:
-opening/saving a file
-file size vs. bit-depth and image-resolution
-calibration
-histograms, “live updates”
-contrast, brightness, saturation
-measurement: linear profiles, statistical information
-Region of Interest (ROI) and local measurements/manipulations
-image calculations 1
http://rsb.info.nih.gov/ijAdapted from : Joel B. Sheffield 2
ImageJ
• An adaptation of NIH image for the Java platform.
• Can run on any computer systems that can run Java (Sun Microsystems)
• Open source
• Two powerful scripting languages
– Java Plugins
– Macro Language
• Continual Upgrades
• Active community of several thousand users
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ImageJ
• Donc, absence de licence coûteuse.
• Pas Besoin d’être à l’université pour faire ses travaux.
• Un portable est amplement suffisant pour 95% de vos besoins.
• Si on besoin de plus de mémoire pour des analyses c’est possible de utiliser l'un des différents serveurs à Laval.
• Supporte plusieurs types de langage de programmation
• Plugins (Interface permettant d'avoir accès à toute la puissance de java. Idéal pour ajouter de nouvelles fonctions à ImageJ)
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Resources
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1. Ferreia, T. et Rasband, W. Ieds) « ImageJ User Guide : IJ1.46r », National Institues of Health,
2012. (lien)
2. Baecker, V. (ed) « Workshop: Image Processing and Analysis with ImageJ », Montpellier RIO
Imaging, 2013. (lien)
3. Miure, K (ed) « Basics of image processing and analysis », Centre for Molecular and Cellular
In this case, the log display indicates that virtually all pixel values are used, even
though they are a small percentage of the total.
Log Scale
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Brightness Adjustment
The brightness adjustment essentially adds or subtracts a constant to every pixel,
causing a shift in the histogram along the x axis, but no change in the distribution37
Contrast Enhancement
For contrast enhancement, a lower value, in this case, 88, is set at zero, and a higher value, 166, is set at 255. The values of each of the pixels are adjusted proportionately. Note that because of the integer values, not all of the pixel values are used. 38
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Addition et soustractionProcess > Math > Add...
Original
-125
+125
Addition et soustraction = modifie la brillance de l'image
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Multiplication et divisionProcess > Math > Multiply...
Original
X 0.5 X 2
Multiplication et division = modifie le contraste de l'image