Skip to content

CLAUDE.md

Latest commit

 

History

History
48 lines (34 loc) · 2.73 KB

CLAUDE.md

File metadata and controls

48 lines (34 loc) · 2.73 KB

CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

What this project is

A Fiji/ImageJ plugin that provides drag-and-drop support for opening OME-Zarr (Open Microscopy Environment – Zarr) image datasets. It supports OME-Zarr v0.4 (Zarr v2) and v0.5 (Zarr v3) and integrates with both ImageJ and BigDataViewer for multi-resolution visualization.

Build and test commands

mvn clean package          # build
mvn test                   # run all tests (requires 2 GB heap – configured in pom.xml)
mvn test -Dtest=ClassName  # run a single test class
mvn test -Dtest=ClassName#methodName   # run a single test method
mvn clean test -Pcoverage  # build with JaCoCo coverage report

Blosc native library is required for tests. On macOS:

brew install c-blosc
export DYLD_LIBRARY_PATH=$(brew --prefix c-blosc)/lib:$DYLD_LIBRARY_PATH
export JAVA_TOOL_OPTIONS=-Djava.library.path=$(brew --prefix c-blosc)/lib

Architecture

Entry point: DnDHandlerPlugin – a SciJava IOPlugin that intercepts drag-and-drop of filesystem paths, checks whether the path is a Zarr folder via ZarrUtils.isZarr(URI), then delegates to ZarrOpenActions.

Core data model: Pyramidal5DImageDataImpl (implements Pyramidal5DImageData) wraps an N5 reader and exposes the multi-resolution pyramid, channel/timepoint metadata, affine transforms, and conversion to BigDataViewer sources or ImageJ datasets.

Opening modes (enum ZarrOpenBehavior in sc.fiji.ome.zarr.open.options):

  • IMAGEJ_HIGHEST_RESOLUTION / IMAGEJ_CUSTOM_RESOLUTION → ZarrOpenActions.openIJWithImage()
  • BDV_MULTI_RESOLUTION → ZarrOpenActions.openBDVWithImage()
  • SHOW_SELECTION_DIALOG → DnDActionChooser Swing dialog with icon buttons

Settings are persisted across Fiji sessions via SciJava PrefService in OpeningBehaviorSettings and UserScriptSettings.

Key utility classes:

  • ZarrUtils – consolidated Zarr-detection utility; isZarr(URI) handles both local filesystem (looks for .zarray / zarr.json) and HTTP (HEAD-requests known metadata files); isHttpAccessible is package-private
  • ClipboardUtils – reads the system clipboard (readClipboard()) and converts strings to URIs (stringToUri(String, Consumer<String>)); readClipboardAsUri(Consumer<String>) combines both
  • BdvHandleService – SciJava service managing the BigDataViewer window lifecycle
  • BdvUtils / Affine3DUtils – BigDataViewer and affine-transform helpers
  • ScriptUtils – opens Fiji script editor with a pre-populated scriptlet

Package root: sc.fiji.ome.zarr

Test resources (sample OME-Zarr datasets) live under src/test/resources/ and are accessed via ZarrTestUtils.resourcePath().