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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)

Project details


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