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Inselect
A tool for the semi-automated segmentation and annotation of specimen trays.
Installation under Microsoft Windows
We provide Microsoft Windows installer packages which can be found on our downloads page. Once installed, Inselect will be available in your Programs Menu. You will need to install the Microsoft Visual C++ 2008 Redistributable Package as well - however this is usually already included on your operating system, so only download it if Inselect fails to start.
If you would like to install the project from source on Windows, you will need to:
- Install Git from http://git-scm.com/download/win ;
- Install Anaconda from http://continuum.io/downloads ;
- Download OpenCV from http://opencv.org/downloads.html (You want a 2.x version) and extract the archive ;
- Copy the file
<open cv extract root>/build/python/2.7/x86/cv2.pydto<anaconda root>/Lib/site-packages(Replace x86 by 64 as appropriate) ; - Open an Anaconda Shell and run
pip install -e git+https://github.com/vls-lab/inselect.git#egg=inselect.
From the Anaconda Shell you can now run Inselect by typing inselect.exe, and the source code is in src\inselect. If you would like to create a Microsoft Installer package, you can do the following:
- Open an Anaconda shell and run (the first time)
pip install cx_Freeze; - cd into
src/inselectand runpython setup.py bdist_msi.
The installer can be found in the dist subdir.
Installation under OSX
-
Install Anaconda
-
Install OpenCV:
conda install -c https://conda.binstar.org/jjhelmus opencv conda install pyside
Installation under Linux (Global)
We do not provide ready-built binaries for Linux. These build instructions will install inselect globally on Ubuntu 12.04-LTS. If you wish to install inselect in a virtual environment, see the instructions in the next section.
apt-get install python-pip git python-pyside python-opencv python-numpy python-scipy python-matplotlib python2.7-dev
pip install git+https://github.com/vls-lab/inselect.git#egg=inselectYou can then run inselect simply with:
inselectInstallation undex Linux (Virtual environment)
These instructions are for Ubuntu 12.04-LTS. Note that there is no functioning build script for OpenCV at this stage, we install globally and copy it into the virtual environment.
apt-get install python-pip git cmake python2.7-dev python-opencv
apt-get build-dep python-matplotlib
apt-get build-dep python-pyside
apt-get build-dep python-scipy
pip install virtualenv
virtualenv inselect
cd inselect
. bin/activate
cp /usr/lib/pymodules/python2.7/cv* ./lib/python2.7/site-packages
pip install git+https://github.com/vls-lab/inselect.git#egg=inselectFrom within the virtual environment, you can then run inselect with:
inselect