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ci: install Fiji mcib3d dependency
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‎.github/workflows/ci.yml‎

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name: CI
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on:
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push:
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branches:
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- main
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- master
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pull_request:
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branches:
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- main
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- master
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permissions:
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contents: read
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jobs:
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build:
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name: Maven build
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runs-on: ubuntu-latest
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steps:
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- name: Check out repository
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uses: actions/checkout@v4
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- name: Set up Java
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uses: actions/setup-java@v4
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with:
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distribution: temurin
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java-version: "8"
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cache: maven
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- name: Install mcib3d-core dependency
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run: |
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curl -fL -o mcib3d-core-4.1.7b.jar https://sites.imagej.net/Tboudier/plugins/mcib3d-suite/mcib3d-core-4.1.7b.jar-20250509161435
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mvn -B install:install-file \
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"-Dfile=mcib3d-core-4.1.7b.jar" \
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"-DgroupId=org.framagit.mcib3d" \
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"-DartifactId=mcib3d-core" \
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"-Dversion=4.1.7b" \
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"-Dpackaging=jar" \
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"-DgeneratePom=true"
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- name: Build and test
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run: mvn -B clean verify "-Denforcer.skip=true"

‎.gitignore‎

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# Build output
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/target/
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mcib3d-core-*.jar
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# IDE files
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/.idea/
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*.iml
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/.vscode/
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/.classpath
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/.project
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/.settings/
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*.swp
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*~
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# OS files
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.DS_Store
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Thumbs.db
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desktop.ini
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# Temp files
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*.tmp.*

‎.zenodo.json‎

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{
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"title": "3D Objects Counter+: morphology-filterable 3D object counting for Fiji/ImageJ",
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"upload_type": "software",
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"description": "A Fiji/ImageJ plugin extending the classic 3D Objects Counter workflow with fixed morphology and intensity filters, macro-recordable options, and a public Java API.",
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"creators": [
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{
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"name": "Malcolm, Jamie",
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"affiliation": "UK Dementia Research Institute at Imperial College London",
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"orcid": "0009-0008-3862-2776"
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}
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],
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"license": "BSD-3-Clause",
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"keywords": [
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"Fiji",
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"ImageJ",
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"microscopy",
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"3D object counting",
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"morphological filtering",
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"segmentation"
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],
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"related_identifiers": [
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{
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"identifier": "https://github.com/Jay2owe/3DObjectsCounterPlus",
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"relation": "isSupplementTo",
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"scheme": "url",
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"resource_type": "software"
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},
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{
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"identifier": "10.1111/j.1365-2818.2006.01706.x",
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"relation": "cites",
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"scheme": "doi",
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"resource_type": "publication-article"
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},
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{
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"identifier": "10.1093/bioinformatics/btt276",
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"relation": "cites",
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"scheme": "doi",
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"resource_type": "publication-article"
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}
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]
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}

‎CHANGELOG.md‎

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# Changelog
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All notable changes to 3D Objects Counter+ are documented here.
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## [0.1.0] - 2026-05-17
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### Added
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- Fiji/ImageJ command at `Analyze > 3D Objects Counter+`.
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- Native-style dialog with threshold and slice controls, live threshold preview,
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fixed morphology/intensity filter ranges, map selection, result-table
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selection, and optional measurement redirect.
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- Public Java API through `OC3DPlus`, `OC3DPlusParameters`, and
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`OC3DPlusResult`.
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- Macro-recordable options for threshold, size limits, edge exclusion,
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measurement redirect, direct morphology filters, and output visibility.
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- Object, surface, centroid, and center-of-mass maps with numbered overlays.
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- Per-object statistics, summary logging, and public macro/API documentation.
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- Streaming filtered measurement path for morphology filters without re-running
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unsafe heavyweight map generation.
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### Fixed
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- Guarded high-fragmentation filtered stacks against ImageJ application stalls
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caused by expensive legacy object-map pathways.
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- Preserved morphology result columns for filtered runs, including filters that
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do not directly use every morphology feature.
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- Kept object-map labels visible regardless of object count by using overlay
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labels instead of changing map pixels.
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- Made measurement redirect use processing snapshots so live ImageJ windows are
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not read while the engine is running.
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### Notes
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- The Fiji update site and Zenodo DOI are not live yet.

‎CITATION.cff‎

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cff-version: 1.2.0
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message: "If you use 3D Objects Counter+ in published work, please cite it as below."
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type: software
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title: "3D Objects Counter+: morphology-filterable 3D object counting for Fiji/ImageJ"
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abstract: >-
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Extension of the classic Fiji 3D Objects Counter (Bolte and Cordelieres,
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2006) with morphological filters (sphericity, compactness, elongation,
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volume, surface area, Feret diameter, intensity), a public Java API,
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and macro-recordable workflows.
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authors:
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- given-names: Jamie
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family-names: Malcolm
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orcid: "https://orcid.org/0009-0008-3862-2776"
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affiliation: "UK Dementia Research Institute at Imperial College London"
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email: jamiemalcolm12@gmail.com
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repository-code: "https://github.com/Jay2owe/3DObjectsCounterPlus"
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url: "https://github.com/Jay2owe/3DObjectsCounterPlus"
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license: BSD-3-Clause
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version: "0.1.0"
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date-released: 2026-05-17
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keywords:
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- fiji
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- imagej
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- microscopy
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- 3d-object-counting
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- morphological-filtering
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- segmentation
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references:
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- type: article
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title: "A guided tour into subcellular colocalization analysis in light microscopy"
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authors:
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- family-names: Bolte
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given-names: S.
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- family-names: Cordelieres
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given-names: F. P.
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journal: "Journal of Microscopy"
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year: 2006
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doi: "10.1111/j.1365-2818.2006.01706.x"

‎LICENSE‎

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Copyright (c) 2026 Jamie Malcolm
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Developed at the Brancaccio Lab, UK Dementia Research Institute,
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Imperial College London.
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are
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met:
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1. Redistributions of source code must retain the above copyright
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notice, this list of conditions and the following disclaimer.
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2. Redistributions in binary form must reproduce the above copyright
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notice, this list of conditions and the following disclaimer in the
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documentation and/or other materials provided with the distribution.
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3. Neither the name of the copyright holder nor the names of its
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contributors may be used to endorse or promote products derived from
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this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
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TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
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PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
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LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
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NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY FROM THE USE OF THIS
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SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

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