Imageanalysistools by cjfuller

ImageAnalysisTools

A java library for prototyping image processing and quantification methods with a focus on biological microscopy

A high-level interface speeds development of new tools. Simple interfaces are preferred over lots of options.

Visit every pixel in an (up to 5D) image:

Image im = ...
for (ImageCoordinate ic : im ) {
  ...
}

All analysis is scriptable using ruby.

include IATScripting

parameter_definitions do
  define_parameter :min_size, 20
end
method_definition do
  filter = get_filter :SizeAbsoluteFilter
  filter.apply(imageset.getMarkerImage)
end

Analysis metadata files are automatically generated that can be executed to repeat the same analysis.

<?xml version="1.0" ?>
<analysis_metadata>
  <input_state>
    <parameters>
      <parameter name="method_name" type="string" value="CentromereFindingMethod">
 ...

For more information on using the project from its GUI see Using ImageAnalysisTools or ask the user google group.

For more information on using the project as a library from your own code see Developing with ImageAnalysisTools or ask the developer google group.