3D Objects Counter+

A Fiji/ImageJ plugin for 3D object counting with native-style controls and fixed min/max morphology filters.

It extends the workflow of the native 3D Objects Counter (Bolte & Cordelieres 2006) by adding filters for object shape, volume, surface area, Feret diameter, and intensity, while keeping the familiar threshold, size-filter, map, statistics, and macro workflow.

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.

What It Adds

• Native-like Analyze > 3D Objects Counter+ dialog.
• Center-slice IsoData threshold as the default starting threshold.
• Live threshold preview on the displayed slice.
• Threshold and slice scrollbars modelled on the native Fiji controls.
• Fixed min/max rows for size and every supported morphology filter.
• Object, surface, centroid, and center-of-mass maps with numbered labels.
• Per-object statistics, native-style summary logging, and progress feedback.
• Macro-recordable command options and a small Java API for batch workflows.

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.
2. Copy it into Fiji's plugins/ folder.
3. Restart Fiji.
4. Run Analyze > 3D Objects Counter+.

When the update site is published, it will be installable from Help > Update... > Manage Update Sites by enabling 3DObjectsCounterPlus.

Use

GUI

Open a 3D stack, then run Analyze > 3D Objects Counter+.

The dialog starts at the centre slice and applies an IsoData threshold from that slice. Adjust Threshold to choose the object cutoff; voxels at or above the threshold are highlighted in the image preview. Use Slice to check the threshold through the stack without running object counting.

Filters are fixed min/max ranges. Defaults do not remove objects:

Filter	Default
Size (Voxels)	10 to stack voxel count
Sphericity	0 to 1
Compactness	0 to 1
Elongation	1 to Infinity
Surface area	0 to Infinity
Mean intensity	0 to Infinity
Max intensity	0 to Infinity
Max Feret diameter	0 to Infinity
Volume	shown only for spatially calibrated images

Preview runs object counting and keeps the dialog open. OK runs object counting, creates the selected outputs, and closes the dialog. The progress bar updates while the full stack is being labelled, measured, and mapped.

Measurement Redirect

Redirect measurements to lets you detect objects on one image while measuring intensity from another open image. Use this when the detection image is a mask or filtered stack, but intensity statistics should come from the raw channel. When a redirect is used, the ImageJ log summary names both images, for example edges.tif redirect to raw.tif: 2 objects detected .... Statistics table and map window titles keep the detection image title.

X/Y/Z are geometric centroid coordinates. XM/YM/ZM are intensity-weighted center-of-mass coordinates. These coordinate sets can be identical when the measurement image is binary or uniform inside each object.

Macro

Run the plugin from an ImageJ macro with the active image selected:

run("3D Objects Counter+", "threshold=128");

Options are whitespace-separated. A full call can combine thresholding, size limits, edge exclusion, redirect, filters, and output controls:

run("3D Objects Counter+",
    "threshold=128 min=20 max=Infinity " +
    "exclude_edges " +
    "sphericity>=0.6 volume>=100 " +
    "redirect=[raw.tif] " +
    "hide_surfaces hide_centroids");

Filters are written directly as macro options using the feature name. Do not wrap them in filter1=, filter2=, or any other numbered option.

Macro options:

Option	Meaning	Default
threshold=<int>	Voxel intensity cutoff for object detection.	0
min=<int>	Minimum object size in voxels.	10
max=<int>	Maximum object size in voxels.	Infinity
max=Infinity or max=inf	No upper size limit.	Infinity
exclude_edges	Exclude objects touching image borders.	Off
redirect=[image title]	Measure intensity and center of mass from another open image.	None
<feature><op><value>	Morphology/intensity filter, for example sphericity>=0.6.	None
hide_labels	Do not show the object label map.	Show
hide_surfaces	Do not show the surface map.	Show
hide_centroids	Do not show the centroid map.	Show
hide_centers_of_mass	Do not show the center-of-mass map.	Show
hide_centres_of_mass	British spelling alias for hide_centers_of_mass.	Show
hide_stats	Do not show the statistics table.	Show
hide_summary	Do not write the ImageJ log summary.	Show

Filter syntax is feature>=value, feature<=value, feature>value, or feature<value. Keep each filter as one token with no spaces. Multiple filters are ANDed, so an object must pass every filter to remain. Up to 64 filters are supported. Indexed filter options such as filter1= are not accepted.

Supported filter features and example macro tokens:

Feature	Meaning	Example
volume	Object volume in voxels.	volume>=100
volume_calibrated	Object volume in calibrated spatial units cubed.	volume_calibrated>=250
surface_area	Surface area in calibrated spatial units squared.	surface_area<=500
sphericity	Shape roundness, typically 0..1.	sphericity>=0.6
compactness	Unitless compactness measure.	compactness<=0.8
elongation	Unitless elongation measure.	elongation<2
mean_intensity	Mean intensity from the source or redirect image.	mean_intensity>=500
max_intensity	Maximum intensity from the source or redirect image.	max_intensity<65535
feret_diameter_max	Maximum 3D Feret diameter in calibrated spatial units.	feret_diameter_max>=5

For example, this keeps objects that pass all three filters:

run("3D Objects Counter+",
    "threshold=128 min=20 sphericity>=0.6 volume>=100 elongation<2");

To save results in a batch macro, select the generated table by its title:

open("/path/to/detection.tif");
imageTitle = getTitle();
run("3D Objects Counter+",
    "threshold=128 min=20 sphericity>=0.6 " +
    "hide_labels hide_surfaces hide_centroids hide_centers_of_mass " +
    "hide_summary");
selectWindow("Results for " + imageTitle);
saveAs("Results", "/path/to/detection_oc3dplus.csv");

For redirect macros, the redirect image must already be open. Use bracketed titles, for example redirect=[raw.tif]. Avoid [ ] quotes, backslashes, or line breaks in image titles used in macro options.

Java

OC3DPlusParameters params = OC3DPlus.builder()
    .threshold(128)
    .minSize(20)
    .addFilter("sphericity", ">=", 0.6)
    .build();

OC3DPlusResult result = OC3DPlus.count(imp, params);

The public Java API lives under sc.fiji.oc3dplus.api. The main entry point is OC3DPlus; results are returned as OC3DPlusResult without opening ImageJ windows or mutating the source image.

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

Maps to show:

• Objects: labelled object map with object numbers at centroids.
• Surfaces: labelled surface-voxel map with object numbers at centroids.
• Centroids: point map at geometric centroids.
• Centers of mass: point map at intensity-weighted centers of mass.

When a run finds thousands of objects, text-number overlays are skipped to keep output map windows lighter. The map pixel labels and statistics table are still produced.

Result tables:

• Statistics: per-object measurements, including native-style columns and morphology quantifications.
• Summary: ImageJ log line with threshold, size range, object count, and morphology means. If measurement redirect is active, the line starts with <detection image> redirect to <measurement image>.

Filtered Processing Notes

For standard single-channel 8-bit or 16-bit stacks, filtered runs use classic 3D Objects Counter labelling first, then apply the Plus filters on that label map with streaming measurements. Object, surface, centroid, and center-of-mass maps are built from the filtered label image and matching statistics table.

Morph_* statistics columns remain available in filtered results. Values that cannot be computed are reported as NaN. Shape values such as sphericity, compactness, elongation, and 3D Feret diameter come from the bounded Plus measurement path, so they can differ slightly from older mcib3d values.

Build

curl -fL -o mcib3d-core-4.1.7b.jar https://sites.imagej.net/Tboudier/plugins/mcib3d-suite/mcib3d-core-4.1.7b.jar-20250509161435
mvn install:install-file "-Dfile=mcib3d-core-4.1.7b.jar" "-DgroupId=org.framagit.mcib3d" "-DartifactId=mcib3d-core" "-Dversion=4.1.7b" "-Dpackaging=jar" "-DgeneratePom=true"
mvn clean package "-Denforcer.skip=true"

The deployable artifact is target/3D_Objects_Counter_Plus-<version>.jar.

Citing 3D Objects Counter+

If you use this plugin in published work, please cite it. Citation metadata is in CITATION.cff. A Zenodo DOI will be added once the first tagged release is archived.

When publishing results that use this plugin, please also cite the upstream tools it builds on:

• 3D Objects Counter by Fabrice Cordelieres and Susanne Bolte (Bolte and Cordelieres, J Microsc, 2006, doi:10.1111/j.1365-2818.2006.01706.x).
• mcib3d-core by Thomas Boudier (Ollion et al., Bioinformatics, 2013, doi:10.1093/bioinformatics/btt276).

License

BSD 3-Clause License. See LICENSE for the full text.

Acknowledgements

Developed by Jamie Malcolm in the Brancaccio Lab at the UK Dementia Research Institute, Imperial College London.

This work was supported by the UK Dementia Research Institute, which receives its core funding from the UK Medical Research Council, the Alzheimer's Society, and Alzheimer's Research UK.

Built on the Fiji / ImageJ ecosystem, Fabrice Cordelieres's 3D Objects Counter, and Thomas Boudier's mcib3d-core.