Python

Object Classification using ilastik

Component
Description

This workflow classifies objects based on object-level features (e.g. intensity based, morphology based, etc) and user annotations. It needs segmentation images besides the raw image data. Segmentation images can be obtained from ilastik pixel classification, or binary segmentation images from other tools. Within the object classification, one can prefilter objects through thresholds (on pixel probability image) or object sizes (on segmentation image). Outputs are predicted classification label images. Selected features can also be exported. Advanced users also have possibilities to add customized (object) features for classification in a simple plugin fashion through python scripts.

has function
Image segmentation
Object classification

Interactive Density Counting using ilastik

Workflow
Description
This workflow estimates (densely distributed) object counts by the density of objects in the image without performing segmentation or object detection. Current version only works for 2D images of roundish objects with similar sizes on relatively homogeneous background. Users should provide a few labels of background and objects (especially on clustered objects), and the tool predicts the density of objects on the entire image. Counting is then estimated by integrating the density values on the whole image or specified rectangular regions of interests.
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Aphelion

Collection
Description

A commercial image analysis software. It's interface allows to easily perform measurements and image analysis. Your actions can be recorded and a macro (in a basic script language) can then be created. Almost no knowledge in programming is needed. You can also use python. A SDK is also available to develop stand alone applications in c++. Additional modules allow to use specific operations (3D operators... Examples of available categories of operators : filtering, edge detection, mathematical morphology, segmentation, Frequency operations, mathematical/logical operations, measurements...

has topic
Bioimage informatics
has function
Image analysis
Image processing
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python-bioformats

Collection
Description
Python-bioformats is a Python wrapper for Bio-Formats, a standalone Java library for reading and writing life sciences image file formats. Bio-Formats is capable of parsing both pixels and metadata for a large number of formats, as well as writing to several formats. Python-bioformats uses the python-javabridge to start a Java virtual machine from Python and interact with it. Python-bioformats was developed for and is used by the cell image analysis software CellProfiler (cellprofiler.org). PyPI record: https://pypi.python.org/pypi/python-bioformats Documentation: http://pythonhosted.org/python-bioformats/ GitHub repository: https://github.com/CellProfiler/python-bioformats Report bugs here: https://github.com/CellProfiler/python-bioformats/issues python-bioformats is licensed under the GPL license to be compatible with the copy of Bio-Formats that is distributed with the package, but is compatible with a BSD license if loci_tools.jar is replaced with SCIFIO jars. See the accompanying file LICENSE for details.
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python-javabridge

Collection
Description
The javabridge Python package makes it easy to start a Java virtual machine (JVM) from Python and interact with it. Python code can interact with the JVM using a low-level API or a more convenient high-level API. PyPI record: https://pypi.python.org/pypi/javabridge Documentation: http://pythonhosted.org/javabridge/ GitHub repository: https://github.com/CellProfiler/python-javabridge Report bugs here: https://github.com/CellProfiler/python-javabridge/issues python-javabridge is licensed under the BSD license. See the accompanying file LICENSE for details.
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