A python package to interactively visualize and process time lapsed volumetric data as generated with modern light sheet microscopes. The package provides a generic 3D+t data viewer as well as denoising and deconvolution methods and makes use of GPU acceleration via OpenCL.

just find the dmg in the download section, open and drag to Applications

you wanna install libtiff to speed up opening of tiff files

brew install libtiff

The app essentially bundles all dependencies and extracts them on the fly so startup might be slow

On Mac, clang might complain about non supported compiler flags, a quick fix to which is

export CFLAGS=-Qunused-arguments

export CPPFLAGS=-Qunused-arguments

install PyQt4, e.g. with homebrew:

brew install pyqt

install libtiff (optional)

brew install libtiff

then with pip

pip install --user git+http://mweigert@bitbucket.org/mweigert/pyocl

pip install --user git+http://mweigert@bitbucket.org/mweigert/spimagine

or the developmental branch

pip install --user git+http://mweigert@bitbucket.org/mweigert/spimagine@develop

1. Make sure you have a working OpenCL configuration.

2. Install dependencies:
   sudo apt-get install python-pyopencl python-opengl python-qt4-gl

3. Checkout this repository

   git clone https://github.com/maweigert/spimagine
   cd spimagine

4. Install required packages

   pip install -r requirements.txt

5. Install spimagine

   python setup.py install

• segmentation fault:
  Uninstall libtiff (pylibtiff) package. See also https://code.google.com/p/pylibtiff/issues/detail?id=11

• Intel GPU and OpenCL: use Beignet. See also maweigert#2

• GPU is not detected by pyopencl
  You might have installed a new version (331.113) of the nvidia drivers. Try installing an older version (331.38), running dpkg-reconfigure, and rebooting again.

• _cl.so: symbol clRetainDevice, version OPENCL_1.2 not defined in file libOpenCL.so.1 with link time reference
  Make sure you have the dependencies of python-pyopencl installed.

• pytools-related ImportError: cannot import name intern
pytools and six versions are not compatible. Try uninstalling pytools via pip and use the system pytools (apt-get install python-pytools)

Run the Qt Gui Application to render 3d/4d Data either via

python -m spimagine

or via the app bundle in the binary folder (currently only for Mac OSX 10.9)

SpImagine.app

Right now the following formats are supported

• tiff files
• 16 bit unsigned raw data in the format used by the Myers Group at mpi-cbg

spimagine_render -h

list the options for the command line tool

the package provides interactive visualisation to be used e.g. within IPython

:::python 
from spimagine import volshow, volfig

data = ...          #3d or 4d numpy array

volfig(0)           #optional: similar behaviour like matplotlib.figure, e.g. can be omitted

volshow(data)       #render the data

interactively:

:::python 
import spimagine 
spimagine.setOpenCLDevice(1)  #optional: set the GPU to use

or put a config file ".spimagine" in your home folder

OPENCLDEVICE = 1