maweigert/biobeam

GPU accelerated beam propagation tools for biological light tissue simulations

biobeam - Fast simulation of image formation for in-silico tissue microscopy

biobeam is an open source python package for simulating light propagation on weakly scattering tissue. It implements a scalar beam propagation method while making use of GPU acceleration via PyOpenCL. It is designed to provide fast wave optical simulations common in light sheet microscopy while providing an easy to use API from within Python.

Among the features are

• Fast vectorial psf calculations for various illumination modes (gaussian.bessel beams, cylindrical lenses, bessel lattices...)
• Fast scalar wave optical simulation of incident light interaction with weakly scattering tissue
• Simulation module for image formation in light sheet microscopy and aberration calculations

Quickstart

First make sure there is a valid OpenCL platform available on your machine, e.g. check with

clinfo

then install everything via pip

pip install biobeam

The full documentation with examples can be found here.

biobeam's Issues

unit of units-parameter in nanometers and not microns?

Hey Martin,

when playing with the method biobeam.focus_field_beam, we had the feeling, that the units parameters expects values in nanometers, but according to the documentation, it's microns. Can you clearify?

Thanks,
Robert

opencl version

Hi,
What is the required opencl version? Will it work with OpenCL 1.2?

Has anyone managed to install it on Windows?

Hi, everyone,
I am trying to install Spimagine or Biobeam on Windows, from Anaconda prompt, without any success.
Did anyone manage this?
My system is Windows 7, Anaconda 64 bit, Python 2.7, OpenCL C 2.0, graphics card Intel HD 520 (CPU, not GPU). Can it work on such configuration in principle?
Thanks!

PS: The errors are:

pip install spimagine
...
    C:\Users\user1\AppData\Local\Programs\Common\Microsoft\Visual C++ for Pyth
on\9.0\VC\Bin\amd64\cl.exe /c /nologo /Ox /MD /W3 /GS- /DNDEBUG -DPYGPU_PACKAGE=
pyopencl -DPYGPU_PYOPENCL=1 -DPYOPENCL_USE_SHIPPED_EXT=1 -Isrc/c_wrapper/ -Ic:\u
sers\user1\appdata\local\continuum\anaconda2\include -Ic:\users\user1\appdat
a\local\continuum\anaconda2\PC /Tpbuild\temp.win-amd64-2.7\Release\pyopencl._cff
i.cpp /Fobuild\temp.win-amd64-2.7\Release\build\temp.win-amd64-2.7\Release\pyope
ncl._cffi.obj -std=gnu++11
    cl : Command line warning D9002 : ignoring unknown option '-std=gnu++11'
    pyopencl._cffi.cpp
    C:\Users\user1\AppData\Local\Programs\Common\Microsoft\Visual C++ for Pyth
on\9.0\VC\Include\stdint.h(82) : error C2371: 'int8_t' : redefinition; different
 basic types
            build\temp.win-amd64-2.7\Release\pyopencl._cffi.cpp(221) : see decla
ration of 'int8_t'
    c:\users\user1\appdata\local\temp\pip-install-pxw3ou\pyopencl\src\c_wrappe
r\clinfo_ext.h(10) : fatal error C1083: Cannot open include file: 'CL/cl.h': No
such file or directory
    error: command 'C:\\Users\\user1\\AppData\\Local\\Programs\\Common\\Micros
oft\\Visual C++ for Python\\9.0\\VC\\Bin\\amd64\\cl.exe' failed with exit status
 2

and

pip install biobeam
...
    C:\Users\user1\AppData\Local\Programs\Common\Microsoft\Visual C++ for Pyth
on\9.0\VC\Bin\amd64\cl.exe /c /nologo /Ox /MD /W3 /GS- /DNDEBUG -DPYGPU_PACKAGE=
pyopencl -DPYGPU_PYOPENCL=1 -DPYOPENCL_USE_SHIPPED_EXT=1 -Isrc/c_wrapper/ -Ic:\u
sers\user1\appdata\local\continuum\anaconda2\include -Ic:\users\user1\appdat
a\local\continuum\anaconda2\PC /Tpbuild\temp.win-amd64-2.7\Release\pyopencl._cff
i.cpp /Fobuild\temp.win-amd64-2.7\Release\build\temp.win-amd64-2.7\Release\pyope
ncl._cffi.obj -std=gnu++11
    cl : Command line warning D9002 : ignoring unknown option '-std=gnu++11'
    pyopencl._cffi.cpp
    C:\Users\user1\AppData\Local\Programs\Common\Microsoft\Visual C++ for Pyth
on\9.0\VC\Include\stdint.h(82) : error C2371: 'int8_t' : redefinition; different
 basic types
            build\temp.win-amd64-2.7\Release\pyopencl._cffi.cpp(221) : see decla
ration of 'int8_t'
    c:\users\user1\appdata\local\temp\pip-install-wkccr_\pyopencl\src\c_wrappe
r\clinfo_ext.h(10) : fatal error C1083: Cannot open include file: 'CL/cl.h': No
such file or directory
    error: command 'C:\\Users\\user1\\AppData\\Local\\Programs\\Common\\Micros
oft\\Visual C++ for Python\\9.0\\VC\\Bin\\amd64\\cl.exe' failed with exit status
 2

    ----------------------------------------
Command "c:\users\user1\appdata\local\continuum\anaconda2\python.exe -u -c "im
port setuptools, tokenize;__file__='c:\\users\\user1\\appdata\\local\\temp\\pi
p-install-wkccr_\\pyopencl\\setup.py';f=getattr(tokenize, 'open', open)(__file__
);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'ex
ec'))" install --record c:\users\user1\appdata\local\temp\pip-record-ms6qyf\in
stall-record.txt --single-version-externally-managed --compile" failed with erro
r code 1 in c:\users\user1\appdata\local\temp\pip-install-wkccr_\pyopencl\

Update installation instructions or dependency information of installed packages?

Hey Martin,

I had some issues getting biobeam running on my Fedora 27. I figured out that I need to run it on Python 3, install pyopencl, intel-opencl-drivers, numpy, scipy and pillow manually.
The scipy/pillow-issue is also discussed here: amueller/mglearn#2
Is there maybe something wrong with the dependency tree? Shouldn't all this (except intel-stuff) come directly with biobeam?

Cheers,
Robert