Skip to content

Latest commit

 

History

History
89 lines (64 loc) · 2.86 KB

README.md

File metadata and controls

89 lines (64 loc) · 2.86 KB
Raw

Lasagna - Python Volume Visualiser for 3-D data.

cover image

Concept

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.

Installation

Lasagna runs on Python 3, PyQt5, and uses PyQtGraph for the plotting and requires the following modules:

  • PyLibTiff
  • pynrrd
  • numpy
  • pyqtgraph >0.10.0
  • MatplotLib
  • yaml [and pyyaml]
  • Scipy [optional - ARA explorer]
  • Scikit-Image [optional - ARA explorer]
  • PyQt5
  • SIP
  • tifffile [optional for importing LSM files]
  • vtk [optional, for faster import of MHD files but doesn't work in Python 3]

On Linux you can install most of the above via your package manager with the remaining packages being installed via pip3 (cd to Lasagna directory to run the pip3 install line) :

apt-get install python3 python3-pip python3-pyqt5 python3-numpy python3-matplotlib
python3-scipy python3-sip
pip3 install -r requirements.txt --user

This command installs the dependencies in your home folder. If you add the --upgrade flag, pip3 will also install newer vesions of packages already in the system path.

There is currently no vtk support in Python 3. If you run into problems try installing the dependencies separately (see below). For other platforms, please see here

On Mac you will first need to Install HomeBrew

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

The install Python 3 and a couple of other packages without which you won't be able to install the rest of the dependencies:

brew install freetype pkg-config python3

Now you can install the dependencies in requirements.txt using: pip3 install -r requirements.txt --user

If for some reason this fails, try installing the dependencies seperately:

pip3 install numpy
pip3 install matplotlib
...

Setup

After the first run, Lasagna creates a preferences 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.

Usage

See the website.

Current status

Even the master branch is currently unstable (although should always be usable).