release: clean public repository surface

Author: Jay2owe

.github/workflows/ci.yml

@@ -0,0 +1,33 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    name: Maven build
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Java
+        uses: actions/setup-java@v4
+        with:
+          distribution: temurin
+          java-version: "8"
+          cache: maven
+
+      - name: Build and test
+        run: ./mvnw -B clean verify -Denforcer.skip=true

.gitignore

@@ -18,10 +18,11 @@
 /.claude/
 CLAUDE_CONTEXT.md
 
-# Internal engineering plan notes (kept on disk, not published)
-/docs/plan/
+# Local/private docs and audit notes (not published)
+/docs/
+/PUBLISHING_AUDIT.md
 
-# Release staging area (drafts for publishing — local only, not published)
+# Release staging area (drafts for publishing - local only, not published)
 /release-staging/
 
 # OS files

.zenodo.json

@@ -0,0 +1,41 @@
+{
+  "title": "3D Objects Counter+: morphology-filterable 3D object counting for Fiji/ImageJ",
+  "upload_type": "software",
+  "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.",
+  "creators": [
+    {
+      "name": "Malcolm, Jamie",
+      "affiliation": "UK Dementia Research Institute at Imperial College London",
+      "orcid": "0009-0008-3862-2776"
+    }
+  ],
+  "license": "BSD-3-Clause",
+  "keywords": [
+    "Fiji",
+    "ImageJ",
+    "microscopy",
+    "3D object counting",
+    "morphological filtering",
+    "segmentation"
+  ],
+  "related_identifiers": [
+    {
+      "identifier": "https://github.com/Jay2owe/3DObjectsCounterPlus",
+      "relation": "isSupplementTo",
+      "scheme": "url",
+      "resource_type": "software"
+    },
+    {
+      "identifier": "10.1111/j.1365-2818.2006.01706.x",
+      "relation": "cites",
+      "scheme": "doi",
+      "resource_type": "publication-article"
+    },
+    {
+      "identifier": "10.1093/bioinformatics/btt276",
+      "relation": "cites",
+      "scheme": "doi",
+      "resource_type": "publication-article"
+    }
+  ]
+}

docs/java-api.md API.mddocs/java-api.md renamed to API.md

@@ -1,4 +1,4 @@
-# 3D Objects Counter+ — Java API
+# 3D Objects Counter+ - Java API
 
 The plugin exposes its engine as a small public API so it can be used as a
 library from any Java code running inside Fiji (or any JVM with the
@@ -16,7 +16,7 @@ necessary jars on the classpath).
 ```
 
 This plugin's only runtime requirements are the native Fiji
-`3D_Objects_Counter` and `mcib3d-core` jars — both supplied by Fiji's core
+`3D_Objects_Counter` and `mcib3d-core` jars - both supplied by Fiji's core
 update site and the standard 3D ImageJ Suite. Once the 3D Objects Counter+
 update site is published, users running that update site should have the
 needed jars.
@@ -27,13 +27,13 @@ All under `sc.fiji.oc3dplus.api`.
 
 | Class | Purpose |
 | --- | --- |
-| `OC3DPlus` | Static façade with `count()`, `detect()`, `countAll()`, `builder()`. |
+| `OC3DPlus` | Static facade with `count()`, `detect()`, `countAll()`, `builder()`. |
 | `OC3DPlus.Builder` | Fluent builder for `OC3DPlusParameters`. |
 | `OC3DPlusParameters` | Immutable parameter bundle. |
 | `OC3DPlusResult` | Per-call result: stats, label image, per-filter survivor counts. |
 | `MorphPredicate` | Single `feature OP value` filter. `parse()` / `format()` for macro use. |
 
-## Example 1 — simple count, no filters
+## Example 1 - simple count, no filters
 
 ```java
 import ij.ImagePlus;
@@ -54,7 +54,7 @@ System.out.println("Objects: " + result.objectCount());
 result.statistics().show("OC3D+ Results");
 ```
 
-## Example 2 — with morph filtering
+## Example 2 - with morph filtering
 
 ```java
 import ij.ImagePlus;
@@ -82,7 +82,7 @@ for (int i = 0; i < labels.length; i++) {
 }
 ```
 
-## Example 3 — headless batch (parallel)
+## Example 3 - headless batch (parallel)
 
 ```java
 import ij.ImagePlus;
@@ -108,11 +108,11 @@ for (int i = 0; i < images.size(); i++) {
 }
 ```
 
-`countAll` shares no state across threads — `params` is immutable and each
+`countAll` shares no state across threads - `params` is immutable and each
 worker constructs its own engine instance. Results are returned in input
 order.
 
-The Java façade methods return `OC3DPlusResult` objects directly. They do not
+The Java facade methods return `OC3DPlusResult` objects directly. They do not
 show images, open table windows, mutate the input image, or write to ImageJ's
 global Results window; callers choose what to display or save. The engine may
 update ImageJ status text while it runs.
@@ -122,7 +122,7 @@ update ImageJ status text while it runs.
 | Feature name | Source | Units |
 | --- | --- | --- |
 | `volume` | `MeasureVolume.getVolumePix` | voxels |
-| `surface_area` | `MeasureSurface.getSurfaceContactUnit` | calibrated² |
+| `surface_area` | `MeasureSurface.getSurfaceContactUnit` | calibrated^2 |
 | `sphericity` | `MeasureCompactness.SPHER_CORRECTED` | unitless 0..1 |
 | `compactness` | `MeasureCompactness.COMP_CORRECTED` | unitless |
 | `elongation` | `MeasureEllipsoid.ELL_ELONGATION` | unitless |

CHANGELOG.md

@@ -0,0 +1,35 @@
+# Changelog
+
+All notable changes to 3D Objects Counter+ are documented here.
+
+## [0.1.0] - 2026-05-17
+
+### Added
+
+- Fiji/ImageJ command at `Analyze > 3D Objects Counter+`.
+- Native-style dialog with threshold and slice controls, live threshold preview,
+  fixed morphology/intensity filter ranges, map selection, result-table
+  selection, and optional measurement redirect.
+- Public Java API through `OC3DPlus`, `OC3DPlusParameters`, and
+  `OC3DPlusResult`.
+- Macro-recordable options for threshold, size limits, edge exclusion,
+  measurement redirect, direct morphology filters, and output visibility.
+- Object, surface, centroid, and center-of-mass maps with numbered overlays.
+- Per-object statistics, summary logging, and public macro/API documentation.
+- Streaming filtered measurement path for morphology filters without re-running
+  unsafe heavyweight map generation.
+
+### Fixed
+
+- Guarded high-fragmentation filtered stacks against ImageJ application stalls
+  caused by expensive legacy object-map pathways.
+- Preserved morphology result columns for filtered runs, including filters that
+  do not directly use every morphology feature.
+- Kept object-map labels visible regardless of object count by using overlay
+  labels instead of changing map pixels.
+- Made measurement redirect use processing snapshots so live ImageJ windows are
+  not read while the engine is running.
+
+### Notes
+
+- The Fiji update site and Zenodo DOI are not live yet.

CITATION.cff

@@ -17,6 +17,7 @@ repository-code: "https://github.com/Jay2owe/3DObjectsCounterPlus"
 url: "https://github.com/Jay2owe/3DObjectsCounterPlus"
 license: BSD-3-Clause
 version: "0.1.0"
+date-released: 2026-05-17
 keywords:
   - fiji
   - imagej
@@ -35,5 +36,3 @@ references:
     journal: "Journal of Microscopy"
     year: 2006
     doi: "10.1111/j.1365-2818.2006.01706.x"
-# TODO: add `doi:` once Zenodo concept DOI is minted from the first
-# tagged GitHub Release.

README.md

@@ -1,5 +1,7 @@
 # 3D Objects Counter+
 
+[![CI](https://github.com/Jay2owe/3DObjectsCounterPlus/actions/workflows/ci.yml/badge.svg)](https://github.com/Jay2owe/3DObjectsCounterPlus/actions/workflows/ci.yml)
+
 A Fiji/ImageJ plugin for 3D object counting with native-style controls and
 fixed min/max morphology filters.
 
@@ -9,7 +11,7 @@ It extends the workflow of the native
 surface area, Feret diameter, and intensity, while keeping the familiar
 threshold, size-filter, map, statistics, and macro workflow.
 
-![3D Objects Counter+ dialog](docs/images/3d-objects-counter-plus-dialog.png)
+![3D Objects Counter+ dialog](assets/3d-objects-counter-plus-dialog.png)
 
 > **Status:** `0.1.0` is a public pre-release. The Fiji update site is planned
 > but not live yet; for now, use a packaged JAR or build from source.
@@ -27,6 +29,12 @@ threshold, size-filter, map, statistics, and macro workflow.
 
 ## Install
 
+Requirements:
+
+- Fiji/ImageJ.
+- The standard Fiji `3D Objects Counter` and `mcib3d-core` dependencies, which
+  are provided by Fiji's core update sites.
+
 Manual install:
 
 1. Build or download `3D_Objects_Counter_Plus-<version>.jar`.
@@ -177,8 +185,18 @@ OC3DPlusParameters params = OC3DPlus.builder()
 OC3DPlusResult result = OC3DPlus.count(imp, params);
 ```
 
-See [docs/java-api.md](docs/java-api.md) for API details and
-[docs/macro-examples.ijm](docs/macro-examples.ijm) for macro examples.
+See [API.md](API.md) for API details and
+[examples/macro-examples.ijm](examples/macro-examples.ijm) for macro examples.
+
+## How It Works
+
+3D Objects Counter+ first labels thresholded 3D objects with the classic Fiji
+3D Objects Counter path. When extra filters are enabled, it measures morphology
+and intensity features from the label map, applies the selected ranges, and then
+builds the requested maps and results from the filtered label image.
+
+This keeps the default no-extra-filter workflow close to the classic plugin
+while avoiding expensive legacy map-generation paths for filtered runs.
 
 ## Outputs