Ensure that you have Xcode installed, for example by running gcc
in the
terminal. Alternatively, you can use the app store.
gcc
Install Homebrew.
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
Install freetype and Python using Homebrew.
brew install freetype
brew install freeimage
brew install python
Install virtualenv
using pip
(virtualenv allows you to create
a virtual Python environment).
sudo pip install virtualenv
Create a virtual environment.
virtualenv env
Source the virtual environment (note the .
at the start of the line).
. ./env/bin/activate
Install Python dependencies into the virtual environment.
pip install numpy
pip install scipy
pip install scikit-image
pip install jicbioimage.core
pip install jicbioimage.transform
pip install jicbioimage.segment
pip install jicbioimage.illustrate
Follow the
jicbioimage installation notes
to install bioformats
.
Download the wheat segementation project from githq and go into it.
Install the Anaconda Python distribution.
Setup a virtual environment named venv
and install the scientific Python
package dependencies.
conda create –n venv python=2.7 numpy scipy scikit-image
Activate the virtual environment.
activate venv
Install the jicbioimage
dependencies.
pip install jicbioimage.core
pip install jicbioimage.transform
pip install jicbioimage.segment
pip install jicbioimage.illustrate
Follow the
jicbioimage installation notes
to install freeimage
and bioformats
.
Download the wheat segementation project from githq and go into it.
On Windows remember to activate the virtual environment when you open a new command prompt.
activate venv
On a Mac/Linux system one activates the virtual environment using the command below.
. ./venv/bin/activate
Run the analysis.
python scripts/wheat_variety_analysis.py /path/to/raw/file/of/interest.lif output_directory
This will produce a file named cell_lengths.csv
in the output directory
along with a number of annotated images. Look at the images and decide if
any series need to be excluded from the cell_lengths.csv
file due to poor
segmentation results.
Use your curated cell_lengths.csv
file as input for your statistical analysis.