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SciJava Command Documentation Status

This document tracks the documentation status of all SciJava commands (@Plugin annotated classes) in the bigdataviewer-image-loaders project.

Total Commands Found: 10 (active, non-deprecated) Fully Documented: 10 Legacy/Deprecated: 4 (not exposed to users)

Fully Documented Commands (10)

These commands have both @Plugin(description=...) and @Parameter(label=..., description=...) for all user-facing parameters.

Bio-Formats Commands (4)

File Description
bioformats/command/CreateBdvDatasetBioFormatsCommand.java Creates a BDV dataset from one or more Bio-Formats compatible files
bioformats/command/CreateBdvDatasetBioFormatsSimpleCommand.java Creates a BDV dataset from a single Bio-Formats compatible file
bioformats/command/BdvShowFileBioFormatsCommand.java Opens a file in BigDataViewer using Bio-Formats, with colors from metadata
bioformats/command/OpenSampleCommand.java Opens a sample dataset from a selection of test images (downloads and caches on first use)

OMERO Commands (3)

File Description
omero/command/CreateBdvDatasetOMEROCommand.java Creates a BDV dataset from one or more OMERO image URLs
omero/command/OmeroConnectCommand.java Connects to an OMERO server using your credentials
omero/command/OmeroDisconnectCommand.java Disconnects from an OMERO server and closes all sessions

QuPath Commands (1)

File Description
qupath/command/CreateBdvDatasetQuPathCommand.java Creates a BDV dataset from all images in a QuPath project

ImagePlus Commands (1)

File Description
imageplus/command/ImagePlusToBdvDatasetCommand.java Creates a BDV dataset from the current ImagePlus window

Utility Commands (1)

File Description
FixFilePathsCommand.java Allows fixing invalid file paths in a BDV dataset by providing replacement paths

Legacy/Deprecated Commands (4)

These commands are marked @Deprecated with their @Plugin annotation commented out. They are not exposed to users but are maintained for backward compatibility with existing code.

File Notes
legacy/bioformats/command/BasicOpenFilesWithBigdataviewerBioformatsBridgeCommand.java Deprecated, @Plugin commented out
legacy/bioformats/command/OpenFilesWithBigdataviewerBioformatsBridgeCommand.java Deprecated, @Plugin commented out
legacy/bioformats/command/StandaloneOpenFileWithBigdataviewerBioformatsBridgeCommand.java Deprecated, @Plugin commented out
legacy/qupath/command/QuPathProjectToBDVDatasetLegacyCommand.java Deprecated, @Plugin commented out

Documentation Guidelines

See DOCUMENTATION_GUIDELINES.md for detailed documentation standards.

Quick Reference

  1. @Plugin annotation - Add description attribute:

    @Plugin(type = Command.class,
        menuPath = "...",
        description = "Brief description of what the command does")

  2. @Parameter annotations - Add label and description for user-facing parameters:

    @Parameter(label = "Input File",
           description = "The image file to open")
File file;

  3. Service parameters - No documentation needed (not user-facing):

    @Parameter
Context context;  // No label/description needed

Last updated: 2025-12-29