Fiji.NET (IKVM-based Fiji + Bio-Formats for .NET 10)

Overview

Fiji.NET provides a way to run Fiji (ImageJ distribution) and Bio-Formats inside a .NET application using IKVM. It enables loading, processing, and converting microscopy images directly from C# without requiring a separate Java runtime environment at execution time.

This project bridges the Java-based imaging ecosystem (ImageJ/Fiji/Bio-Formats) with modern .NET applications such as BioGTK, BioImager, and other microscopy workflows.

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⚠️ Important Compatibility Note

This project is based on the last Java 8–compatible Fiji stack.

Implications:

• Uses legacy ImageJ + SciJava ecosystem versions
• Newer Fiji / ImageJ2 features (Java 11+) are not available
• Some plugins may not function under IKVM
• SciJava command discovery is partially limited

This tradeoff is required because IKVM targets Java 8 bytecode compatibility.

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Key Features

• Run Fiji/ImageJ inside .NET via IKVM
• Load microscopy formats using Bio-Formats
• Access ImagePlus objects directly in C#
• Support for hundreds of scientific image formats (NDPI, OME-TIFF, CZI, etc.)
• No external Fiji installation required at runtime
• Targeted for .NET 10
• Simple installation via NuGet

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Installation (NuGet)

The recommended way to use Fiji.NET is via NuGet:

dotnet add package Fiji.NET

This automatically includes:

• Required Fiji / ImageJ jars
• SciJava dependencies
• Bio-Formats (bioformats_package.jar)
• IKVM configuration

No manual jar management is required.

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Architecture

.NET 10 (C#)
   ↓
IKVM Runtime
   ↓
Fiji / ImageJ (Java 8)
   ↓
Bio-Formats
   ↓
Microscopy Images

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Usage

Initialize ImageJ (optional UI)

ij.ImageJ ijm = new ij.ImageJ();

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Load an image using Bio-Formats

ij.ImagePlus[] imps = loci.plugins.BF.openImagePlus("test.ome.tif");
ij.ImagePlus imp = imps[0];

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Access pixel data

var processor = imp.getProcessor();
int width = imp.getWidth();
int height = imp.getHeight();

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Notes

• Bio-Formats is used directly via API (loci.plugins.BF)
• Fiji is embedded and does not require a separate installation
• Designed for programmatic use rather than full plugin-driven workflows

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Recommended Strategy

For stability:

• Use the NuGet package (avoid manual jar setup)
• Use Bio-Formats API directly

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Summary

Fiji.NET enables:

• Reliable microscopy image loading in .NET 10
• Seamless access to Bio-Formats
• Integration with modern .NET imaging tools

Best practice:

Use Bio-Formats as a library, not as a plugin system, when running under IKVM.

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Credits

• ImageJ / Fiji
• Bio-Formats (OME)
• SciJava ecosystem
• IKVM