ImageJ / Fiji

ImageJ is a free, open-source program for scientific image analysis, and Fiji is its “batteries-included” distribution with hundreds of plugins already installed. In dentistry it is a research and teaching tool rather than a clinical viewer: people use it to measure distances, areas and gray values on radiographs, photographs and histology slides, and to analyse bone structure with plugins such as BoneJ.

If you are looking for an ImageJ download, most dental researchers today install Fiji, because it bundles Java, the updater and the DICOM and microscopy importers. Both are free for any use.

ImageJ / Fiji at a glance

What it does

• Opens common image formats (TIFF, JPEG, PNG and more) and some kinds of DICOM directly. In Fiji, the Bio-Formats importer adds support for many microscopy and medical formats.
• Spatial calibration with Analyze > Set Scale. You draw a line over an object of known length, enter the real distance, and all later measurements are in millimetres instead of pixels.
• Measures length, angle, area, perimeter, mean gray value and other statistics for any region of interest (ROI). Results go to a table you can export to a spreadsheet.
• Density calibration with Analyze > Calibrate, so gray values can be converted using known reference standards (for example a step wedge in the image).
• Thresholding, filters, particle analysis and colour deconvolution for histology and microscopy images.
• Stacks: works with image series and 3D volumes, with orthogonal views and 3D rendering available in Fiji.
• Macros and scripting (ImageJ macro language, plus Python/Jython, JavaScript and others in Fiji) to process hundreds of images the same way.
• Update sites add extra plugins. For example, BoneJ adds bone analysis such as trabecular thickness and anisotropy.

How dental teams use it

Relative bone density on radiographs

1. Open the radiograph (exported as TIFF or DICOM) at full resolution, with no JPEG compression if possible.
2. Draw the region of interest, for example periapical bone or an extraction site, and use Analyze > Measure to record the mean gray value.
3. Measure a reference region on the same image, such as cortical bone or a step wedge, and compare the two values.

A 2025 study in the journal Dentistry Journal used ImageJ 1.54i in exactly this way to estimate relative bone density on orthopantomograms. Gray values depend on exposure and processing, so compare only images taken under the same conditions.

Trabecular analysis around implants (research)

Install BoneJ through Help > Update > Manage update sites, binarise the region of interest, and run the trabecular measurements. A 2023 study in the International Journal of Dentistry used ImageJ with BoneJ on periapical radiographs of an animal implant model to track density, trabecular thickness, separation and number during osseointegration.

Linear measurements for theses and audits

1. Calibrate with Set Scale using an object of known size in the image, or use the pixel spacing stored in the DICOM file.
2. Use the straight-line tool for distances, such as crestal bone levels relative to an implant shoulder, and the angle tool for angulations.
3. Press M after each line and save the Results table as CSV for statistics.

Histology and photographs

Threshold stained sections to measure area fractions (for example new bone versus graft material), count cells with Analyze Particles, or measure shade and gingival areas on standardised clinical photographs.

Install and first run

• Fiji on Windows: extract the archive into your user folder, for example C:Users[name]Fiji. The Fiji team warns against C:Program Files, because the updater then runs into permission problems. The “Latest” build needs Windows 10 or later.
• Fiji on macOS: the “Latest” build supports macOS 11 Big Sur or later, on both Apple Silicon and Intel, with Java included in the download.
• Fiji on Linux: the “Latest” build targets Ubuntu 22.04 LTS or later on x86-64 or arm64.
• Stable vs Latest: “Stable” still uses Java 8 and runs on old systems, including 32-bit Windows. “Latest” uses Java 21. Most users should choose Latest.
• Plain ImageJ 1.x: bundles are offered with Java 8 for Windows, Intel Macs and Linux, and with a newer OpenJDK for Apple Silicon Macs. Update it with Help > Update ImageJ.
• Memory: for large CBCT stacks, raise the memory limit in Edit > Options > Memory & Threads.

Limitations

• It is a research tool, not a clinical DICOM workstation. There is no PACS connection, no patient database and no panoramic or cross-sectional dental reformatting.
• DICOM support is partial. Built-in import reads “some kinds” of DICOM; compressed or multi-frame CBCT exports may need Bio-Formats or a third-party plugin.
• Measurements are only as good as the calibration. A radiograph without a known scale or pixel spacing gives pixel values, not millimetres.
• No regulatory clearance is claimed; it is not intended for diagnosis.

ImageJ / Fiji vs alternatives

FAQ

Is ImageJ free to download?

Yes. ImageJ 1.x is in the public domain and Fiji is open source under the GPL. There is no paid edition.

ImageJ vs Fiji: which should I download?

Fiji is ImageJ plus a large set of preinstalled plugins, an updater and a bundled Java runtime. Choose Fiji unless you specifically want the minimal ImageJ 1.x build.

Is there ImageJ for Mac?

Yes. Fiji “Latest” runs natively on Apple Silicon and Intel Macs with macOS 11 or later, and there is also an ImageJ 1.x bundle for Apple Silicon.

Does ImageJ work on Windows 11?

Yes. Fiji “Latest” requires Windows 10 or later, on x86-64 or arm64. Install it in your user folder, not in Program Files.

Can I use ImageJ online?

Yes: ImageJ.JS, a browser version of ImageJ 1.x from the ImJoy team, runs without installation. For large files and plugins, desktop Fiji is more practical.

Can ImageJ open dental X-rays and CBCT DICOM files?

It opens many DICOM files through File > Open or the Bio-Formats importer. It is suited to measurement and research, not to clinical CBCT review.

How do I measure in millimetres in ImageJ?

Draw a line over something of known length, open Analyze > Set Scale, enter the known distance and unit, then measure. DICOM files often carry their own pixel spacing.

Last checked against official sources: 28 September 2026 (developer website: imagej.net). Versions and licence terms change — confirm on the developer's site before deploying in a clinic.