Skip to main content

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


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

quantan-0.0.23.tar.gz (124.5 kB view hashes)

Uploaded source

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor NVIDIA NVIDIA PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page