imagej 0.3.0

Python wrapper for ImageJ

Python wrapper for ImageJ

imagej.py provides a set of wrapper functions for integration between ImageJ and Python.

It also provides a high-level entry point imagej.IJ for invoking ImageJ Server APIs; see "ImageJ Server" below for details.

Requirements

default:
- imglyb

Install imglyb using conda install -c hanslovsky imglyb.

Further information regarding imglyb can be found in the imglyb GitHub repository.

Usage

In this example, replace /Applications/Fiji.app with the location of your Fiji installation.

# Spin up ImageJ.
import imagej
ij = imagej.init('/Applications/Fiji.app')

# Import an image with scikit-image.
import skimage
from skimage import io
# NB: Blood vessel image from: https://www.fi.edu/heart/blood-vessels
img = io.imread('https://www.fi.edu/sites/fi.live.franklinds.webair.com/files/styles/featured_large/public/General_EduRes_Heart_BloodVessels_0.jpg')
import numpy as np
img = np.mean(img, axis=2)

# Invoke ImageJ's Frangi vesselness op.
vessels = np.zeros(img.shape, dtype=img.dtype)
import imglyb
ij.op().filter().frangiVesselness(imglyb.to_imglib(vessels), imglyb.to_imglib(img), [1, 1], 20)

See also test/test_imagej.py for other examples of usage.

ImageJ Server

Requirements

imagej_server:
- requests
- Pillow

Use pip install -r server_requirements.txt to install requirements for server.

Pillow is required for the imagej.server module's IJ.show() function. In addition, display or xv needs to exist in your system to view the image.

Usage

There is a short usage example here.