Author: Bob Dougherty (firstname.lastname@example.org) Installation: Download Layers_.java or Layers_.class and place it in the Plugins folder. Description: ImageJ plugin to overlay slices of a stack to make a composite image.
Slices are renderd in order, starting with the first one. The content of each slice covers the previously added slices. Areas with the background color are rendered transparently.
Usage: Create or open a stack of images.
A way to get started is to open several images; one background and other images containg elements to be added. Set the background color to the one you want to be transparent. Use Edit->Options->Background Color... or select the eyedropper tool and alt-click on the background color. Blue would be an interesting choice. The background color appears as the square border of the eyedropper tool. Starting with the background image, create a stack using the plugin Stack Sorter to isolate the other elements and add them to the stack with "Insert." Isolate things by using an ROI to select just the interesting parts.
Make the stack the active window and Run or Compile and Run... Layers. A new window appears with the composite image. Arrange the windows so that you can see both the stack and the composite widow. In the stack, choose a slice with an inserted object, and move it to its proper postion by watching the composite window. One way to move something is to draw a box around it with, say, the rectangle tool and then press ctrl-x and then ctrl-v. An arrow-cursor appears, and you can drag the item around the image. (If a box is left where the item originally was, it means you don't have the background color set right.) Do not try to edit the composite image directly; it is continually being computed from the stack. Continue with the other slices.
Another way to make a stack is begin with a single image, set the background color, and add a second slice with Image->Stacks->Add Slice. Now create annotations on this new slice using the Text tool and drawing tools on the Toolbar. (ctrl-d draws ROIs in the foreground color, and Edit->Fill fills them.)
Nicolas Roggli's and Wayne Rasband's Stack Builder brovides yet another way to gather mlutiple images into a stack. Before or after running Layers, select the important parts of the images, set the background color, and use Edit->Clear Outside to free up space. Stack Sorter may be helpful for ajusting the order of the slices.
The plugin continues to run, using significant computer resources, until either the stack or the composite image is closed. Saving the stack makes it easy to resume editing later. The composite image can be saved as final output.
Version 0: 3/12/2004
The plugin may not work well or at all with floationg point images. Convert the stack to another type.
Copyright (c) 2004, 2005, OptiNav, Inc.
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ImageJ: ImageJ can be freely downloaded from the ImageJ web site.