Lasagna is a lightweight platform for visualising for 3D volume data. Lasagna features a flexible plugin system, allowing it to be easily extended using Python and PyQt. Visualisation is peformed via three linked 2D views. Lasagna was written to explore registration accuracy of 3D data, guide registration, and overlay point data onto images. It was also written to help explore the Allen Reference Atlas. Lasagna is under heavy development but is maturing rapidly. For more information see the website.
Lasagna runs on Python 2.7, PyQt4, and uses PyQtGraph for the plotting and requires the following modules:
- tifffile [for importing LSM files]
- vtk [optional, for faster import of MHD files]
- PyLibTiff
- pynrrd
- numpy
- pyqtgraph 0.9.10
- yaml [and pyyaml]
- Scipy [optional - ARA explorer]
- Scikit-Image [optional - ARA explorer]
- PyQt4
- SIP
On Linux you can install everything but PyQt and SIP by running:
pip install -r requirements.txt or pip install --user -r requirements.txt to install in .local/
For other platforms, please see here
After the first run, Lasagna creates a preferenes file in the .lasagna hidden directory in your home directory.
You may need to edit this file to make Lasagna aware of its built in-plugins. i.e. edit the pluginPaths preference.
This step isn't user-friendly, sorry.
See the website.
Even the master branch is currently unstable (although should always be usable).