Stack Contrast Adjustment Plugin



Jan Michalek (michalek at biomed dot cas dot cz)

Martin Capek (capek at biomed dot cas dot cz)

Jiri Janacek (janacek at biomed dot cas dot cz)



Download Stack_Contrast_Adjustment.jar, change its name to and uncompress to retrieve the source code.



Drag and drop Stack_Contrast_Adjustment.jar to the "ImageJ" window, when "Save Plugin..." dialog appears, we recommend to put the file in the plugins>Stack folder. Or download the .jar file to the ImageJ>plugins>Stack folder directly and use Help>Refresh Menus command. The plugin will then be in the Plugins>Stacks menu item.



Fluorescent images captured by a confocal laser scanning microscope (CLSM) from deep layers of a specimen are often darker than images from the top layers due to absorption and scattering of both excitation and fluorescent light. These effects cause problems in subsequent analysis of biological objects. The plugin implements an algorithm for brightness matching of CLSM image stacks, based on aligning distribution functions of image pairs.


Prior processing the user should choose and make active by the slider one slice of the stack - an image with high contrast - as a reference image. Contrast and brightness of images in the stack is adjusted according to this reference image. The reference image stays intact.


This plugin is designed to perform processing on 8-bit grayscale and RGB images.


Dialog box parameter:

Unmark Is background black? checkbox if images in the stack are inverted in intensities, i.e. their background is white.


The dialog shows the number of the active slice that is used as the reference image.


A PDF document and sample confocal stacks (human placenta and rat muscles) are available.



[1] Michalek, J. - Capek, M. - Kubinova, L.: Fast Algorithm for Matching of Image Pairs for Constant Brightness Applied to Stacks of Confocal Microscope Images. Unpublished.


[2] Capek, M. - Janacek, J. - Kubinova, L.: Methods for Compensation of the Light Attenuation with Depth of Images Captured by a Confocal Microscope. Microscopy Research and Technique. 2006, 69(8): 624-635, DOI: 10.1002/jemt.20330


See also: Our plugin PlaneBrightnessAdjustment.





Fig. 1. Subset of a series of optical sections of a human placenta captured by a confocal microscope. The distance between sections in the subset is about 3 microns. The numbers in the figure depict numerical order of optical sections in the full series.



Fig. 2. Corrected subset of a series of confocal optical sections of a human placenta.