Usage Instructions
Starting
See the installation guide for getting started. To get a feel for the viewer with some demo, data start Lasagna with the -D flag.
Loading data
Lasagna currently accepts only single-channel 3D data that can be loaded completely into RAM. Data may be in the form of TIFF stacks or MHD files. Go to File > Load ingredient and select New base stack. A "base stack" is the first 3D image stack to be loaded. All other data, such as overlaid image stacks or points, are added on top of this base stack. Whenever a new base stack is loaded, any other plotted or loaded data are discarded.
Navigating 3D data
Once a base stack is loaded you may navigate it with the mouse:
- Pan by left-clicking and dragging one of the 2-D views. The other two views follow the view being panned.
- Mouse wheel to zoom all three views in and out.
- Explore different slices within one 2-D view by ctrl-wheel. Go faster with shift-ctrl-wheel
- Dynamically slice the other two views by ctrl-dragging (i.e. ctrl+left mouse+drag). The other two axes will show two orthogonal slices taken at the planes of the X and Y cross-hairs. As the cross-hairs are moved across the image, the slices shown in the other two plots update automatically.
- If you lose the sample due to zooming out too much, hit the reset (green circular arrow) button in the toolbar
Changing image properties
You can change the intensity range of the image by moving the sliders on the histogram. There is an opacity slider below the histogram. You may change the color map by right-clicking on the layer name in the "Image" tab and selecting a different colour map. From here you may also delete the layer.
Overlaying data
You may overlay another volume via File > New Base Stack. Once an overlay is loaded, the first loaded layer turns red and the new layer is shown in green. Overlapping regions are yellow. You may change the colours by right clicking on the layers. You may also change the automatic colouring as more layers are added by editing the configuration file in /home/dir/.lasagna
Using plugins
Plugins are independent pieces of Python code that modify the behavior or functionality of Lasagna. Plugins are started by selecting them from the plugin menu. Once started, a tick sybol appears next to the plugin's entry in the menu. Plugins can be stopped by unchecking the menu or, where appropriate, closing the plugin's window.
Preferences
When Lasagna is first loaded it creates a .lasagna hidden directory in your home directory. This contains a plain text configuration file called lasagna_prefs.yml. The contents of this file are fairly self-explanatory and you may edit it. Parameters from the file can be loaded as needed during run time. So in some cases your changes will take effect right away.
Users wishing to add new preferences should look at the lasagna_helperFunctions module and see lasagna.showFileLoadDialog() for an example of how preferences are read and written. Some basic Python knowledge is needed to do this.