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A Medical Image Analysis Package

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BioImage Suite Web -- Python Package

This is package exports much of functionality in BioImage Suite Web as a python package. This requires Python v3.5 or later.

You can invoke all modules from the commandline using the globally installed executable biswebpy. For example to run the image smoothing algorithm type

biswebpy smoothImage -h

The modules are also available for inclusion in your own code under the namespace biswebpython. The same smoothing filter, for example, can be imported as:

from biswebpython.core.bis_objects import *
from biswebpython.modules.smoothImage import *

# Create and load an image
input=bisImage();
input.load(_SOME_INPUT_FILENAME_);
print('Input=',input.getDescription());

# Create and execute the smoothing module
smooth=smoothImage();
smooth.execute( { 'input' : input }, { 'sigma' : 4.0, 'debug' : True });

# Get and save the output
output=smooth.getOutputObject('output');
print('Output=',output.getDescription());
out.save(_SOME_OUTPUT_FILENAME_);

For more information on bisweb see:

You may also take a look at the examples repository https://github.com/bioimagesuiteweb/examples.

BioImage Suite Web (bisweb) is a web-based medical image analysis suite primarily geared towards Neuroimaging Analysis. We gratefully acknowledge support from the NIH Brain Initiative under grant R24 MH114805 (Papademetris X. and Scheinost D. PIs).

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