The new plugins can then be found under Plugins Beat. (use an Explorer (not the Internet Explorer), enter the address and log in by giving "anonymous" as the user name and type your email address for the password.) For adding the library to ImageJ, please follow the instructions in the "ReadMe.txt" file. They can be freely visualized and downloaded from the official Wiki of ImageJ at which is also containing a comprehensive description of all plugins included to the library, or from the Empa ftp server at The ImageJ plugins are included into the library file "xlib_.jar". Each one of the available tools and its advantage is shortly being presented below. The reason for this apparent re-duplication is that the original tools incorporate major restrictions which are eliminated in the newplugins. Those tools are for instance “FFT”, “Image Calculator”, “Distance Transform” and others. The user might be surprised to realize that some of the tools apparently are already existing in other plugins of ImageJ or Fiji. However, we consider the help button as a handy feature. This feature does not correspond with the ImageJ philosophy assuming the help documentation to be available on the internet. 3D processing may include slice-wise 2D processing of all images in the stack or, more important, true 3D processing.Įach one of the new plugins includes a help button where general remarks about the functionality and a description of the parameters are provided. 3D image data in ImageJ is represented by image stacks. Since the research focus of our group is on 3D imaging, all of our plugins are able to deal with either 2D or 3D image data. The plugins include automated imaging tools for filtering, data reconstruction, quantitative data evaluation and data import, as well tools for interactive segmentation, visualization and management of image data. This macro converts them to 8 bit RGB color.A set of prospective ImageJ plugins is maintained by the group for 3D-Microscopy, Analysis and Modelling of the Laboratory for Concrete and Construction Chemistry at Empa. Raw data used in this webpage downloadable here.Ĭolor brightfield images are often collected by taking red, green, and blue individual images and saving them in series. If you want automation like this, please contact me. Here is a sample macro that changes the colors of channels of a single Z slice file with a single click or keystroke and automatically montages the channels. The displayed channels (and colors and contrast ranges) may be programmed in a macro so that they do not have to be manually set for each image that is opened. The color of any channel may be changed without altering the raw data by making the channel active and then using Image > Lookup Tables. The pixel value at the cursor location diplayed in the status bar and measured intensity values are of the active channel exclusively. The active channel may be changed by moving the "C" slider and the color of the active channel is displayed as the text color at the top of the image. The contrast of each channel may be adjusted independently using the Image > Adjust > Brightness/Contrast tool. The check boxes turn displayed channels on and off. To display mutiple colors at once, use Image > Color > Channels Tools to select which channels you want to see. It may be displayed as the first Z slice in the first channel. This preserves original bit depth, dynamic range, and color LUTs. When you first import a multichannel Z series into ImageJ or FIJI is should be a hyperstack of multiple channels and multiple Z slices.
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