imglyb-examples

This is a repository of examples for imglyb.

Dependencies

All dependencies will be installed automatically when installing imglyb-examples through conda.

• imglyb
• numpy
• scikit-image

imglyb is available on conda or you can install it manually following the build instructions. All other depdendencies are available through your package manager, pip, or various anaconda channels.

Install

Manual

First, make sure that all dependencies are installed, then run

python setup.py install

Conda

conda install -c hanslovsky imglyb-examples

If imglyb was not previously installed, re-source the current conda environment after installing to set the environment properly.

Run

These examples are available.

# bash
# Basic visualization and application of Python and ImgLib2 filters
python -m imglyb_examples.butterfly
# Python implemented overlays for BigDataViewer
python -m imglyb_examples.bdv_hello_world
# Python implementation of a painting tool for BigDataViewer
python -m imglyb_examples.bdv_painter
# Embed BigDataViewer in Qt application (only Linux, and Qt and python-xlib dependencies)
python -m imglyb_examples.qt_awt
# Basic visualization of series of 2D NumPy arrays
python -m imglyb_examples.views_stack

I recommend starting your own code from these examples and extend as you need. On Linux and Windows you can run these commands like this, as well:

imglyb-examples.butterfly
imglyb-examples.bdv-hello-world
imglyb-examples.bdv-painter
mglyb-examples.qt-awt
imglyb-examples.views-stack