Python

  • Python is a general purpose programming language. Over the last few years, more and more tools developed in Python for bioimage analysis and this looks set to continue and increase.
  • Both CellProfiler and Ilastik are written in Python. Jython is an implementation of the Python programming language designed to run on Java platforms so can be used within ImageJ-FIJI.
Facility Resources
  • We plan to create guides for using Python for image analysis. Once complete, they will be found here or as videos here.
  • More general information on image analysis concepts and terms, like classification, can be found here.
External resources
  • The RMS Image Analaysis Focused Interest Group (IAFIG) ran a Python for Image Analaysis course in December 2019. You can see the materials for that here along with a general Python introduction course here. The course is due to rerun December 2020.
  • A YouTube playlist introducing image analysis in Python.
  • Some libraries, frameworks and other tools, commonly used for bioimage analysis workflows are listed below. Some are more general mathematical or data analysis tools while some have been specifically developed with image analysis in mind: Napari (an image viewer for Python), ImagePy, scikit-image, pandas, NumPy, SciPy, matplotlib, Seaborn, Jupyter.
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