Hyperstacks enable ImageJ to handle multidimensional images up to 5D images (width x height x channels x slices x frames i.e. xyczt). To avoid unnecessary duplication of raw files, this plugin allows to load multiple 3D files (width x height x slices x channels) as 5D hyperstacks.
Create a new stack using the File > New > Virtual 5D Stack command. Select by which dimension you would like to load the image files (t or z) and fill in the appropriate size. For each t (or z) level, load the images to populate the remaining dimension.
The plugin:
- Increases the canvas size to the maximum image size in the set.
- Populates missing images as black empty images labelled
missing.
When loading a Virtual 5D Stack, you might want to sort the images along the z dimension. Use the Plugins > Virtual 5D Stack > Sort V5s to create a montage and drag and drop the images to swap their position. You can also drag an image outside the canvas (left or right side) to increase the dimension. To remove a specific z level, drag an image outside the canvas (top or bottom side). A dialog window is shown in order to confirm the suppression of the level (no dialog is shown if the level is empty, i.e. contains only missing images).
Use the command File > Save as > Virtual 5D Stack ... to save the v5s file. A v5s is a xml file containing the informations to reload the 5D hyperstack as it is displayed from the individual raw images.
It is possible to store regions of interest (ROI) directly in a v5s file Plugins > Virtual 5D Stack > ROI > Store ROI. The plugin will ask to attribute a name to the ROI set. Actually, it is only possible to store a single ROI for each slice. To reload a ROI, use the command Plugins > Virtual 5D Stack > ROI > Load ROI. The advantage of storing ROIs in a v5s file is to keep the ROI in sync when using the Sort V5s plugin.