Author: Benjamin Schmid(Bene.Schmid at gmail.com), Johannes Schindelin (Johannes.Schindelin at GMX.DE) History: 2008/07/13: First public version Limitation: Installation: Download VIB_Protocol.jar to the plugins folder, or subfolder, restart ImageJ, and there will be a new command in the Plugins menu, "VIB Protocol". Description:
The VIB Protocol is designed for aligning 3D image stacks. The images we used are confocal images of adult fly brains, but basically the VIB protocol can be used for any 3D images.
The workflow is thereby as follows:
The VIB Protocol starts with the following dialog:
A configuration file stores all the settings for running the VIB Protocol on a particular data set. It is saved in the output directory. If one wants to run the algorithm a second time, it is possible to load (and modify) the previous configuration. If you run this for the first time, just leave the text field blanc and click OK.
After that, a second dialog appears, which asks the user for all the necessary input:
The different fields have the following meaning:
|Files:||Use the buttons "Add to files" and "Delete from files" to add here the input images.|
|Working directory:||All the output of the VIB Protocol goes into this folder.|
|Template:||Choose one of the images in the "Files" list as a template (reference) brain (by selecting it in the list and clicking "Use as template"). Alternatively, you can choose an external reference by typing the path to the file you want to use.|
|No of channels||The number of channels contained in the input files.|
|No of reference channel||The number of the reference channel. The reference channel will be used for labelling.|
|Resampling factor||In order to speed up execution time, it is a good idea to scale the images down. Selecting here '2' for example means that a 1024x1024x256 images will be downsampled to 256x256x64.|
Normally, the Segmentation Editor opens during the software execution and asks the user to label the brains. This step is omitted if there exists already a folder called 'labels' in the output directory and if this folder contains for each image the corresponding labels image. After that, no more user interaction is required, and the software finishes after some time. All the results can be found in the output directory. The structure of this directory is as follows:
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