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SciJava Command Documentation Status

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

Total Commands Found: ~70 Fully Documented: ~65 (with @Plugin description + @Parameter labels/descriptions) Partially Documented: ~3 (has @Plugin description but may need review) Needs Documentation: ~2

Fully Documented Commands (~65)

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

SPIM Data Commands (9)

File Description
spimdata/LLS7OpenDatasetCommand.java Opens a Zeiss LLS7 dataset with live deskewing
spimdata/CreateCZIDatasetCommand.java Creates BigStitcher-compatible XML from CZI
spimdata/FuseBigStitcherDatasetIntoOMETiffCommand.java Fuses BigStitcher dataset to OME-TIFF
spimdata/OpenOperettaDatasetCommand.java Opens PerkinElmer Operetta dataset
spimdata/LLS7CropCommand.java Crops 3D region from LLS7 sources
spimdata/ReorderDatasetCommand.java Reorders LIF dataset (legacy)
spimdata/DatasetToBigStitcherDatasetCommand.java Converts BDV to BigStitcher format
spimdata/RemoveDisplaySettingsCommand.java Removes display settings from BDV dataset
spimdata/RemoveEntitiesCommand.java Removes entities from BDV dataset
spimdata/SourceFromImagePlusCommand.java Converts ImagePlus to BDV dataset
spimdata/OpenImarisCommand.java Opens Imaris .ims files

BDV Commands (8)

File Description
bdv/userdefinedregion/GetUserPointsCommand.java Interactive point selection in BDV
bdv/userdefinedregion/GetUserRectangleCommand.java Interactive rectangle selection in BDV
bdv/userdefinedregion/BoxSelectorCommand.java Interactive 3D box selection in BDV
bdv/BdvViewToImagePlusExportCommand.java Exports current BDV view to ImagePlus
bdv/BasicBdvViewToImagePlusExportCommand.java Simple BDV view to ImagePlus export
bdv/OverviewerCommand.java Creates overview visualization of sources
bdv/ShowGridBdvCommand.java Displays sources in a grid layout
bdv/CurrentBdvSetTimepointsNumberCommand.java Sets timepoint count in BDV slider

PairRegistration Commands - Warpy Workflow (12)

File Description
registration/PairRegistrationCreateCommand.java Creates a new registration pair from fixed and moving sources
registration/PairRegistrationAddGUICommand.java Opens a BDV window with controls for performing registrations
registration/PairRegistrationDeleteCommand.java Removes a registration pair from memory
registration/PairRegistrationCenterCommand.java Applies a translation to center moving sources over fixed sources
registration/PairRegistrationSift2DAffineCommand.java Automatic 2D affine registration using SIFT feature matching
registration/PairRegistrationElastix2DAffineCommand.java Automatic 2D affine registration using Elastix
registration/PairRegistrationElastix2DSplineCommand.java Automatic 2D B-spline deformable registration using Elastix
registration/PairRegistrationBigWarp2DSplineCommand.java Interactive manual landmark-based spline registration
registration/PairRegistrationEditLastRegistrationCommand.java Re-opens the last registration step for editing
registration/PairRegistrationRemoveLastRegistrationCommand.java Removes the last registration step
registration/PairRegistrationExportToOMETIFFCommand.java Exports registered images as pyramidal OME-TIFF
registration/PairRegistrationExportToQuPathCommand.java Exports registration transforms to QuPath project

Source Export Commands (2)

File Description
source/ExportToImagePlusCommand.java Exports sources to ImagePlus ignoring spatial location
source/ExportToMultipleImagePlusCommand.java Exports sources to multiple ImagePlus respecting locations

Source Manipulation Commands (8)

File Description
source/FilterSourcesByNameCommand.java Filters sources by name pattern
source/SourceTimeShiftCommand.java Creates time-shifted source
source/SourcesPyramidizerCommand.java Generates pyramid levels for sources
source/SourcesMakeModelCommand.java Creates model source spanning multiple sources
source/GetVoronoiEllipseSampleCommand.java Creates sample Voronoi ellipse source
source/SliceSourceCommand.java Resamples sources to oblique slice
source/SourceSetAlphaCommand.java Sets L1 alpha blending for sources
source/SourcesFuserAndResamplerCommand.java Fuses and resamples sources

Source Deconvolution Commands (1)

File Description
source/deconvolve/SourcesDeconvolverCommand.java GPU-accelerated Richardson-Lucy deconvolution

Source Registration Commands (11+ including abstract classes)

File Description
source/register/AffineTransformCreatorCommand.java Creates affine transform from matrix
source/register/Elastix2DSplineRegisterCommand.java 2D B-spline registration using Elastix
source/register/Sift2DAffineRegisterCommand.java 2D affine registration using SIFT
source/register/SourcesAffineTransformCommand.java Applies affine transform to sources
source/register/SourcesRealTransformCommand.java Applies real transform to sources
source/register/SelectSourcesForRegistrationCommand.java Abstract base for registration source selection
source/register/Abstract2DRegistrationInRectangleCommand.java Abstract base for 2D ROI registration
source/register/AbstractElastix2DRegistrationInRectangleCommand.java Abstract base for Elastix ROI registration
source/register/WarpyEditRegistrationCommand.java Edit existing Warpy registration
source/register/WarpyExportRegisteredImageCommand.java Export Warpy registered image to OME-TIFF
source/register/WarpyMultiscaleRegisterCommand.java Automated multiscale Warpy registration
source/register/WarpyRegisterCommand.java Interactive Warpy registration wizard

Transform Commands (13)

File Description
transform/RemoveZOffsetCommand.java Removes Z offset from sources
transform/SourcesRecenterCommand.java Recenters sources to specified coordinates
transform/Rotation3DTransformCommand.java Interactive 3D rotation transform
transform/EditSourcesWarpingCommand.java Edit warping transform with BigWarp
transform/Rot3DReSampleCommand.java 3D resampling using ROI points
transform/DisplayEllipseFromTransformCommand.java Creates ellipsoid visualization source
transform/Elliptic3DTransformCreatorCommand.java Creates new elliptical 3D transform
transform/Elliptic3DTransformerCommand.java Applies elliptical transform to sources
transform/Elliptic3DTransformExporterCommand.java Exports elliptical transform to JSON
transform/Elliptic3DTransformImporterCommand.java Imports elliptical transform from JSON
transform/Optimize3DEllipticalTransformCommand.java Optimizes elliptical transform parameters
transform/ExportEllipticProjection.java Exports elliptic projection to ImagePlus
transform/EasyExportEllipticProjection.java Interactive elliptic projection export

Partially Documented Commands (~3)

These commands may need review for complete documentation.

File Notes
source/register/Elastix2DAffineRegisterCommand.java Inherits from abstract, check all params
source/register/Elastix2DSparsePointsRegisterCommand.java Check all params documented
source/register/MultiscaleRegisterCommand.java Check all params documented

Commands Needing Documentation (~2)

These commands may still need documentation review.

File Notes
source/register/RegisterWholeSlideScans2DCommand.java Complex command, needs review
source/register/Wizard2DWholeScanRegisterCommand.java Complex wizard command

Documentation Guidelines

When documenting commands, add:

  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 = "Select Source(s)",
           description = "The source(s) to process")
SourceAndConverter<?>[] sources;

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

    @Parameter
SourceService source_service;  // No label/description needed

Style Guidelines

  • Labels: Use Title Case, 2-4 words
  • Descriptions: Complete sentences, user-friendly language
  • Avoid jargon: Use "image source" instead of "SourceAndConverter"
  • Use "world coordinates units" instead of "physical units"

Last updated: 2025-12-26