MxPlot.Extensions.Tiff 0.0.3-alpha

MxPlot.Extensions.Tiff

OME-TIFF and ImageJ-compatible hyperstack I/O support for MxPlot

MxPlot.Extensions.TIFF provides advanced TIFF read/write capabilities for MatrixData<T>. It is designed to handle 5D bio-imaging data (XY + Channel, Z, Time) with full metadata preservation, bridging MxPlot with the scientific imaging ecosystem (ImageJ/Fiji, Bio-Formats).

Features

• 5D Hyperstack Support: Natively handles multidimensional data (Channel, Z-Slice, Time-Frame).
• Dual Export Strategies:
  • OME-TIFF: Embeds OME-XML metadata (physical pixel size, time intervals, UUIDs) for robust data exchange.
  • ImageJ TIFF: Writes ImageJ-specific tags for immediate, lightweight drag-and-drop compatibility with Fiji.
• Physical Space Awareness: Preserves physical units (e.g., µm) and automatically handles coordinate system conversion (Bottom-Left vs Top-Left).
• Flexible Architecture: Implements MxPlot's IMatrixDataWriter / IMatrixDataReader interfaces.

Components

Based on the internal file structure:

• OmeTiffFormat: The core writer strategy for generating OME-compliant TIFFs.
• ImageJTiffFormat: The writer strategy optimized for ImageJ compatibility.
• OmeTiffHandler / ImageJTiffHandler: High-level I/O handlers.
• ImageJMetadata: Helper class for managing ImageJ specific TIFF tags.

Quick Usage

This library integrates with the MatrixData.Save method via the Strategy Pattern.

Saving Data

using MxPlot.Core;
using MxPlot.Extensions.Tiff;

// Assume 'matrix' is a MatrixData<float> with 5D dimensions (e.g., C=3, Z=24, T=100)
// and physical scaling (e.g., 0.1um/pixel).

// 1. Save as OME-TIFF (Recommended for archival/analysis)
// Preserves full physical metadata and dimension order.
matrix.Save("simulation_data.ome.tif", new OmeTiffFormat());

// 2. Save as ImageJ Hyperstack (Recommended for quick viewing)
// Lightweight format specifically tuned for Fiji.
matrix.Save("quick_view.tif", new ImageJTiffFormat());

// 3. Save with custom options (e.g., disable Y-flip)
var options = new OmeTiffFormat.Options
{
	FlipY = false // Keep original coordinate system
};
matrix.Save("no_flip.ome.tif", new OmeTiffFormat(options));

Loading Data

// Automatically detects OME-TIFF or Standard TIFF and restores axes information.
IMatrixData loadedData = MatrixData.Load("input.ome.tif");

Technical Notes

• Supported Types: byte, sbyte, short, ushort, int, float, double.
• Coordinates: The library automatically handles the vertical flip (Y-axis) required to map MxPlot's mathematical Cartesian coordinates to the raster scan order of TIFF images. This behavior can be customized via the FlipY option if needed. See the API documentation for OmeTiffFormat and ImageJTiffFormat for details.
• Dependencies: Built on top of BitMiracle.LibTiff.NET.

License MIT License