Established workflows#
Minimal
Cite workflow & platform
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Key settings
Key settings are specific settings of variable parameters that largely affect the outcome of the workflow when the settings are changed, for a given program and version. For example, the spot diameter setting in Trackmate is a key setting that may largely change the tracking results with a slightly different setting. The choice of algorithm for particle linking is also a key setting. If the exact same settings are used as the referenced workflow, it is possible to omit them, but writers should be aware that readers will be more likely to use and cite their work if they can utilize their protocol!
WARNING Users should be careful that the overall defaults have not been changed by an administrator, for example a single installation of Fiji used by multiple users may have left over settings changes (like “Invert”) that significantly impact the analysis workflow.
Example data
Example data is required for testing the workflow and the outcome, for peers to study the behavior of the workflow and evaluate its scientific adequacy.
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Manual ROIs
If manualy annotated ROIs are used in the workflow, those ROIs should be saved as a separate file and uploaded as part of the workflow package. In ImageJ, manualy created ROIs can be stored in ROI manager and saved as a file via the menu associated with ROI Manager.
Exact version
If the workflow used is published with version tracked code in a public repository e.g. GitHub, the release date or the exact verion of the code should be present in the methods section or supplementary material section. If the workflow is from a commertial software package, the version of the package and the name of the worlflow must appear in the manuscript. If the workflow is only published as a supplementary material, cite that publication.
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Recommended
All settings
Sharing all settings is fairly straightforward in many cases - where a pipeline can be exported or a macro recorded - but can be tricky in others when certain impactful settings are “hidden” within Preferences or Settings sections of the software - for example Fiji has settings that change both the appearance (Invert LUT) and the values (Invert) of images, which may not be part of a given workflow but still can impact the results. Thus it is beneficial to list as much about the “state” of the program as possible, generally in the supplements as the lists can be quite long.
Public example
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Ideal
Document usage (e.g. screen recording or tutorial)
Including screengrabs of key steps in a pipeline, or if the option is available, a whole video (which could be a link to a hosted video, for example on YouTube or Google Drive) can make it far easier to reproduce an experiment, even a purely digital one. There are frequently steps or intermediate results experienced users take for granted, that may not be obvious to newer users of a given software or pipeline - these things can be captured in a full video recording of use but might be missed in a writeup.
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Cloud hosted or container
The method reproducibility is best ensured with a workflow code included in a container e.g. Docker container, that allows the exact reproduction of the environment for running the workflow code together with the example data. The image of that container can be shared as the reproducible workflow. Otherwise, a publicly accessible exexutable environment e.g cloud hosted server can be prepared to let others to run the workflow code.