A hacky spline drawing program for measuring features in EM images
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
doc
sabl_mpl
.gitignore
LICENSE.md
README.md
setup.cfg
setup.py

README.md

sabl_mpl

Usage

sabl.py [-p w] [-discard h r] [-nspline n] [-alpha a] image_file.png 

Description

"sabl_mpl.py" is a simple spline drawing program which uses the matplotlib gui. It was intended to be used to measure the curvature of cell membranes in electron microscopy images. It has some features to make it convenient to repetitively measure many distances and angles in any 2-D image manually. It requires python and matplotlib to be installed in advance. (This software was featured in Yao et al. EMBO J. (2017), DOI 10.15252/embj.201696235)

Images showing how to use it are located in the "docs" directory, as well as detailed usage and installation instructions.

(NOTE: You must click using the MIDDLE mouse button to draw and make measurements)

Note:

This is a graphical program which must be invoked from a terminal. (When doing so, do not use "&".)

Requirements

This program requires python 2.6 or later. It also requires that the "matplotlib" python module is installed. As with all linux and unix programs, this script must be copied to a directory which is located in your PATH. (For more information see "Installation Details" at the end of this file.)

Installation Instructions

There are two ways to install sabl_mpl:

Installation using pip

If you are familiar with pip, then run the following command from within the directory where this README file is located:

pip install .

Make sure that your default pip install bin directory is in your PATH. (This is usually something like ~/.local/bin/ or ~/anaconda3/bin/. If you have installed anaconda, this will be done for you automatically.) Later, you can uninstall sabl_mpl using:

pip uninstall sabl_mpl

Manual Installation method:

Alternatively, you can edit your PATH variable manually to include the subdirectory where the sabl.py script is located, as well as the subdirectory where most of the python scripts are located. Suppose the directory with this README file is named ``sabl_mpl'' and is located in your home directory:

If you use the bash shell, typically you would edit your ~/.profile, ~/.bash_profile or ~/.bashrc files to contain the following lines:

export PATH="$PATH:$HOME/sabl_mpl/sabl_mpl"

License

sabl_mpl is available under the terms of the open-source 3-clause BSD license. (See LICENSE.md.)