mripy

MRI ImageJ related python (jython) package.

• api-doc

ijmpy

ijmpy is a jython wrapper of the imagej-macro-language. It allow to easily porting macros to jython by reimplementing the macro commands in jython.

The idea is to be able to import ijmpy, copy your ij-macro code and use it in jython, profiting from the python language and datastructures.

Try for example:

  run("Duplicate...", " ");
  run("Find Edges");
  run("8-bit");
  run("Smooth");
  setAutoThreshold(thresholdMethod);
  run("Analyze Particles...", "size="+minSize+"-"+maxSize+" circularity=0.00-1.00 show=Masks exclude in_situ");
  run("Create Selection");
  run("Enlarge...", "enlarge=" + numberOfDilates + " pixel");
  roiManager("Add");
  close();
  roiManager("select", 0);
  run("Clear Outside");

bialang

bialang is a bio-image analyst centric jython wrapper for the ImageJ1 api. In bialang the above code will look something like this:

  image = duplicate(inputImage)
  findEdges(image)
  to8Bit(image)
  smooth(image)
  toMask(image,
     percentileThreshold(image),
     Filter(minSize, maxSize, minCirc, maxCirc, exclude))
  roi = createSelection(image)
  close(image)
  enlarge(roi, numberOfDilates, unit=units.pixel)
  clearOutside(inputImage, roi)

The operations like duplicate, findEdges, ... are implemented as functions and as objects which can be created and configured before run.

For example:

Duplicate = Duplicate()
Duplicate.selectChannels(1, 3)
Duplicate.setZSices(1, 3, 5, 7)
Duplicate.run(image)

bialangsj

bialangsj (sj for sci-java) is a bio-image analyst centric jython wrapper for the ImageJ2 api. The idea is to create the same classes and functions as in bialang but implemented in ImageJ2 and sci-java.

How to use it

Clone or download the repository. Copy the mripy-folder into the folder jars/Lib of your FIJI installation. Import the module you want to use in your iython image analysis script.

from mripy.ijmpy import *

from mripy.bialang import *
from mripy.bialangsj import *

or

from mripy import bialang as bl
from mripy import bialangsj as blsj

Have a look at the unit tests for code-examples.

Notes:

21.02.2020: Currently it's only the beginning of a proove of concept.

Since run, roiManager and setAutoTreshold are implemented in ijmpy, some recorded ij-macros might already work. Please contact me if you want to participate in the project.