SciJava Ops: An Improved Algorithms Framework for Fiji and Beyond

This page serves as a stable location for the SciJava Ops Paper and associated resources. If you find SciJava Ops useful, please cite our (forthcoming) paper:

Python (scyjava)

This use case illustrates the ease with which SciJava Ops can be accessed in Python, showcasing OpEnvironment setup and simple image processing. The full workflow can be found in the scyjava use case.

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3D 3T3 Mouse Nucleus

Fluorescence Lifetime Image Analysis

This use case illustrates how SciJava Ops can be freely extended with additional algorithms libraries, making use of the SciJava framework for convenience and performance in FLIM analysis. The full workflow can be found in the FLIM use case.

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BPAE cells

Spatially Adapted Colocalization Analysis

This use case illustrates the novel scientific utility of the SciJava Ops Image library using powerful algorithms for pixel colocalization. The full workflow can be found in the SACA use case.

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HeLa cell expressing HIV gene products

Deconvolution

This use case illustrates the novel scientific utility of the SciJava Ops Image library using powerful algorithms for image deconvolution. The full workflow can be found in the deconvolution use case.

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3D HeLa nucleus