Quantitative histological analyser
Project description
# QuantAn
Quantitative Analyser
[Sample data](http://147.228.240.61/queetech/sample-data/biodur_sample.zip)
# Install
## Windows
* Use [installer](http://147.228.240.61/queetech/install/setup_quantan.exe)
(experimental)
or
* Install [Anaconda for python 2.7](https://www.continuum.io/downloads)
* Install QuantAn
conda install -c mjirik -c SimpleITK quantan
## Linux (Ubuntu 14.04)
* Install prerequisites
sudo apt-get install cmake libinsighttoolkit3-dev libpng12-dev libgdcm2-dev git wget
wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
source Miniconda-latest-Linux-x86_64.sh
conda install numpy scipy pip imtools io3d sed3
* Install [skelet3d package](https://github.com/mjirik/skelet3d)
git clone https://github.com/mjirik/skelet3d.git
cd skelet3d
mkdir build
cd build
cmake ..
make
sudo make install
pip install .
* Install Quantan
conda install -c mjirik -c SimpleITK quantan
## Mac OS
* Install prerequisites (brew packages, anaconda)
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
brew install git cmake homebrew/science/insighttoolkit libpng
curl "http://repo.continuum.io/miniconda/Miniconda-latest-MacOSX-x86_64.sh" -o "Miniconda-latest.sh"
bash Miniconda-latest.sh -b
echo "export PATH=$HOMEDIR/miniconda/bin:\$PATH" >> ~/.profile
* Install [skelet3d package](https://github.com/mjirik/skelet3d)
git clone https://github.com/mjirik/skelet3d.git
cd skelet3d
mkdir build
cd build
cmake ..
make
sudo make install
cd ..
pip install .
* Install Quantan
conda install -c mjirik -c SimpleITK quantan
# Run
Run QuantAn with:
python -m quantan
![img](http://147.228.240.61/queetech/www/quantan01.png)
![img](http://147.228.240.61/queetech/www/quantan03.png)
![img](http://147.228.240.61/queetech/www/quantan08.png)
![img](http://147.228.240.61/queetech/www/quantan10.png)
# Sample outputs
* [segmentation (DICOM)](http://147.228.240.61/queetech/www/segmentation.dcm)
* [skeleton (DICOM)](http://147.228.240.61/queetech/www/skeleton.dcm)
* [labeled skeleton (DICOM)](http://147.228.240.61/queetech/www/labeled_skeleton.dcm)
Quantitative Analyser
[Sample data](http://147.228.240.61/queetech/sample-data/biodur_sample.zip)
# Install
## Windows
* Use [installer](http://147.228.240.61/queetech/install/setup_quantan.exe)
(experimental)
or
* Install [Anaconda for python 2.7](https://www.continuum.io/downloads)
* Install QuantAn
conda install -c mjirik -c SimpleITK quantan
## Linux (Ubuntu 14.04)
* Install prerequisites
sudo apt-get install cmake libinsighttoolkit3-dev libpng12-dev libgdcm2-dev git wget
wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
source Miniconda-latest-Linux-x86_64.sh
conda install numpy scipy pip imtools io3d sed3
* Install [skelet3d package](https://github.com/mjirik/skelet3d)
git clone https://github.com/mjirik/skelet3d.git
cd skelet3d
mkdir build
cd build
cmake ..
make
sudo make install
pip install .
* Install Quantan
conda install -c mjirik -c SimpleITK quantan
## Mac OS
* Install prerequisites (brew packages, anaconda)
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
brew install git cmake homebrew/science/insighttoolkit libpng
curl "http://repo.continuum.io/miniconda/Miniconda-latest-MacOSX-x86_64.sh" -o "Miniconda-latest.sh"
bash Miniconda-latest.sh -b
echo "export PATH=$HOMEDIR/miniconda/bin:\$PATH" >> ~/.profile
* Install [skelet3d package](https://github.com/mjirik/skelet3d)
git clone https://github.com/mjirik/skelet3d.git
cd skelet3d
mkdir build
cd build
cmake ..
make
sudo make install
cd ..
pip install .
* Install Quantan
conda install -c mjirik -c SimpleITK quantan
# Run
Run QuantAn with:
python -m quantan
![img](http://147.228.240.61/queetech/www/quantan01.png)
![img](http://147.228.240.61/queetech/www/quantan03.png)
![img](http://147.228.240.61/queetech/www/quantan08.png)
![img](http://147.228.240.61/queetech/www/quantan10.png)
# Sample outputs
* [segmentation (DICOM)](http://147.228.240.61/queetech/www/segmentation.dcm)
* [skeleton (DICOM)](http://147.228.240.61/queetech/www/skeleton.dcm)
* [labeled skeleton (DICOM)](http://147.228.240.61/queetech/www/labeled_skeleton.dcm)
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