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Add 3D Objects Counter+ plugin page
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‎_pages/plugins/3d-objects-counter-plus.md‎

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---
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title: 3D Objects Counter+
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description: 3D object counting in Fiji/ImageJ with fixed min/max filters for morphology, volume, Feret diameter, and intensity.
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categories: [Analysis, 3D, Particle Analysis]
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source-url: https://github.com/Jay2owe/3DObjectsCounterPlus
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update-site: 3DObjectsCounterPlus
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release-version: 0.1.0
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release-date: 2026-05-17
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dev-status: Active
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support-status: Active
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team-maintainers: '@Jay2owe'
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license-url: https://github.com/Jay2owe/3DObjectsCounterPlus/blob/main/LICENSE
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license-label: BSD-3-Clause
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---
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3D Objects Counter+ is a Fiji/ImageJ plugin for counting and measuring thresholded 3D objects in image stacks. It extends the native [3D Objects Counter](/plugins/3d-objects-counter) workflow with fixed min/max filters for object shape, volume, surface area, Feret diameter, and intensity.
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The plugin is designed for users who want the familiar threshold, size-filter, map, statistics, measurement redirect, and macro workflow of 3D Objects Counter, with additional morphology filters before the final maps and result tables are created.
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## Installation
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3D Objects Counter+ is distributed through the ImageJ update site:
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{% include link-banner url="https://sites.imagej.net/3DObjectsCounterPlus/" %}
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To install it:
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1. Start Fiji.
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2. Choose {% include bc path="Help|Update..." %}.
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3. Click **Manage update sites**.
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4. Click **Add Unlisted Site**, or enable **3DObjectsCounterPlus** if it is already listed.
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5. Use:
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- Name: `3DObjectsCounterPlus`
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- URL: `https://sites.imagej.net/3DObjectsCounterPlus/`
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6. Apply changes and restart Fiji.
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After restart, run the command from:
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```text
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Analyze > 3D Objects Counter+
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```
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## Main Workflow
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Open a 3D stack, then run **Analyze > 3D Objects Counter+**. The dialog opens with the title `3D Objects Counter+`.
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The main controls are:
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- `Image`, which shows the stack that will be counted.
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- `Threshold`, which sets the voxel-intensity cutoff for object detection.
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- `Slice`, which changes the displayed z-slice while checking the threshold.
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- `Filters:`, which contains fixed `Min` and `Max` ranges.
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- `Exclude objects on edges`, which removes objects touching the stack border.
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- `Maps to show:`, with `Objects`, `Surfaces`, `Centroids`, and `Centers of mass`.
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- `Results tables to show:`, with `Statistics` and `Summary`.
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- `Redirect measurements to:`, which measures intensity from another open image while detecting objects from the active image.
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- `Preview`, `OK`, and `Cancel` action buttons.
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The help button opens `About 3D Objects Counter+ Controls`, which explains the dialog controls, filter meanings, maps, result tables, and action buttons.
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## Threshold And Preview
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The dialog starts on the center slice and uses a center-slice IsoData threshold as the initial value. Changing `Threshold` or `Slice` updates the threshold display so voxels at or above the threshold can be inspected before object counting is run.
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`Preview` runs object counting with the current settings, shows the selected preview maps, and keeps the dialog open. Preview map windows are prefixed with `[Preview]`. `OK` runs object counting with the current settings, opens the selected final outputs, records macro options when the ImageJ macro recorder is active, and closes the dialog.
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## Filters
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Filters are fixed min/max ranges. The default ranges are non-excluding, so objects are only removed when a user tightens a minimum or maximum value.
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The available filter rows are:
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- `Size (Voxels)`, with default minimum `10` and maximum set to the stack voxel count.
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- `Sphericity`, from `0` to `1`.
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- `Compactness`, from `0` to `1`.
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- `Elongation`, from `1` to `Infinity`.
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- `Volume (<unit>^3)`, shown only when the image has calibrated spatial units.
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- `Surface area`, from `0` to `Infinity`.
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- `Mean intensity`, from `0` to `Infinity`.
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- `Max intensity`, from `0` to `Infinity`.
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- `Max Feret diameter`, from `0` to `Infinity`.
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Multiple filters are combined with AND logic, so an object must pass every active range to remain in the final result.
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## Measurement Redirect
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`Redirect measurements to:` lets the active image define the detected objects while another open image supplies intensity measurements and intensity-weighted centers of mass. This is useful when object detection is performed on a mask, filtered stack, or segmentation image, while intensity should be measured from a raw channel.
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The redirect image must already be open and must match the detection image width, height, and stack depth.
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## Outputs
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3D Objects Counter+ can create these map windows:
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- `Objects map of <image>`, a labelled object map with object numbers at centroids.
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- `Surfaces map of <image>`, a labelled surface-voxel map with object numbers at centroids.
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- `Centroids map of <image>`, a point map at geometric centroids.
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- `Centers of mass map of <image>`, a point map at intensity-weighted centers of mass.
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It can also create:
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- `Results for <image>`, a per-object statistics table.
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- An ImageJ log summary reporting the threshold, size range, object count, and morphology means.
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The statistics table includes native-style measurements such as integrated density, mean, standard deviation, minimum, maximum, centroids (`X`, `Y`, `Z`), centers of mass (`XM`, `YM`, `ZM`), bounding-box fields, object labels, and morphology columns such as `Morph_Sphericity`, `Morph_Compactness`, `Morph_Elongation`, and `Morph_Feret3D_um`.
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For very high object counts, text-number overlays can be skipped to keep map windows lighter. The map pixel labels and statistics table are still produced.
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## Supported Inputs
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The interactive command works on the active Fiji/ImageJ image. It expects a non-empty image stack for 3D object counting. Standard Fiji installations provide the underlying ImageJ image model and the native 3D Objects Counter components used by the plugin.
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Calibrated volume filtering appears when the image has real spatial calibration units rather than pixel-only units. Intensity filters and centers of mass are measured from the detection image unless a redirect image is selected.
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## Macro Usage
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3D Objects Counter+ is macro-recordable and can be called from ImageJ macros:
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```ijm
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run("3D Objects Counter+", "threshold=128");
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```
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A fuller call can combine thresholding, size limits, edge exclusion, measurement redirect, morphology filters, and output visibility:
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```ijm
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run("3D Objects Counter+",
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"threshold=128 min=20 max=Infinity " +
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"exclude_edges sphericity>=0.6 volume>=100 " +
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"redirect=[raw.tif] hide_surfaces hide_centroids");
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```
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Supported direct filter tokens include `volume`, `volume_calibrated`, `surface_area`, `sphericity`, `compactness`, `elongation`, `mean_intensity`, `max_intensity`, and `feret_diameter_max`. Supported operators are `>=`, `<=`, `>`, and `<`.
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Output windows can be hidden with `hide_labels`, `hide_surfaces`, `hide_centroids`, `hide_centers_of_mass`, `hide_stats`, and `hide_summary`. The British spelling `hide_centres_of_mass` is also accepted.
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## Java API
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The public Java API lives under `sc.fiji.oc3dplus.api`. The main entry point is `OC3DPlus`, with parameters built through `OC3DPlusParameters` and results returned as `OC3DPlusResult`.
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```java
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OC3DPlusParameters params = OC3DPlus.builder()
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.threshold(128)
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.minSize(20)
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.addFilter("sphericity", ">=", 0.6)
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.build();
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OC3DPlusResult result = OC3DPlus.count(imp, params);
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```
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The API can count one image or process lists of images without opening ImageJ result windows.
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## Runtime Dependencies
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The plugin requires Fiji/ImageJ and uses the standard Fiji 3D object-counting stack. The update site records dependencies on ImageJ, `mcib3d-core`, the native `3D_Objects_Counter`, and `Colocalization_Image_Creator`, so normal update-site installation resolves the runtime files.
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## Citing
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When publishing work that uses 3D Objects Counter+, cite the plugin using the citation metadata in the source repository. Please also cite the upstream tools it builds on: the original 3D Objects Counter work by Bolte and Cordelieres, and the mcib3d work by Ollion and colleagues.

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