ZarrNET 0.1.1

Zarr.NET

A high-performance, fully async C# library for reading and writing OME-Zarr datasets with comprehensive support for multiscale images, labels, and High-Content Screening (HCS) plate data.

Features

✅ Zarr v2 & v3 Support - Automatic version detection and handling
✅ OME-Zarr 0.4 & 0.5 - Full spec compliance for multiscale images, labels, and HCS plates
✅ Remote Access - Read from HTTP/HTTPS, S3, Azure Blob, Google Cloud Storage
✅ Physical Coordinates - ROI reading in real-world units (micrometers, seconds, etc.)
✅ Compression - Gzip, Zstandard (zstd) codec support
✅ Memory Efficient - Chunk-level reading with streaming support
✅ Type Safe - Strongly typed metadata models and coordinate transformations
✅ Cross-Platform - .NET 10.0, works on Windows, Linux, macOS
✅ Well-Architected - Clean separation of concerns, testable, extensible

Installation

# Via NuGet (when published)
dotnet add package ZarrNET

# Or clone and build locally
git clone https://github.com/yBiologyTools/ZarrNET.git
cd ZarrNET
dotnet build

Dependencies

• .NET 10.0 or higher
• ZstdSharp.Port (managed zstd implementation)
• System.Text.Json (included in .NET 8.0)
• AForgeBio

Quick Start

Read a single 2D plane from a multiscale image

using ZarrNET;
using ZarrNET.Helpers;

await using var reader = await OmeZarrReader.OpenAsync("/path/to/dataset.zarr");
var image = reader.AsMultiscaleImage();
var level = await image.OpenResolutionLevelAsync(datasetIndex: 0);

// Read timepoint 0, channel 1, z-slice 5
var plane = await level.ReadPlaneAsync(t: 0, c: 1, z: 5);

// Get as typed 2D array
ushort[,] pixels = plane.As2DArray<ushort>();  // for uint16 data
Console.WriteLine($"Plane: {plane.Width}x{plane.Height}, max value: {pixels.Cast<ushort>().Max()}");

// Or get as byte array for interop
byte[] bytes = plane.ToBytes<ushort>(PixelFormat.Gray8);

Read using physical coordinates (ROI in microns)

using ZarrNET.Coordinates;

// Define ROI: 100µm x 100µm region at specific location
var roi = new PhysicalROI(
    origin: [0, 0, 5.0, 50.0, 50.0],    // t, c, z, y, x in physical units
    size:   [1, 1, 1.0, 100.0, 100.0]   // timepoint, channel, z-slice, 100µm x 100µm
);

var result = await level.ReadRegionAsync(roi);

Read from remote HTTP/S3 URLs

// Public HTTP server
var httpUrl = "https://example.com/datasets/image.zarr";
await using var reader = await OmeZarrReader.OpenAsync(httpUrl);

// S3 public bucket
var s3Url = "https://s3.amazonaws.com/bucket/image.zarr";
await using var s3Reader = await OmeZarrReader.OpenAsync(s3Url);

// Azure Blob Storage
var azureUrl = "https://account.blob.core.windows.net/container/image.zarr";
await using var azureReader = await OmeZarrReader.OpenAsync(azureUrl);

// Works exactly the same as local files
var image = reader.AsMultiscaleImage();
var plane = await level.ReadPlaneAsync(t: 0, c: 0, z: 0);

Custom HTTP configuration (auth, timeouts)

using OmeZarr.Core.Zarr.Store;

var httpClient = new HttpClient();
httpClient.DefaultRequestHeaders.Add("Authorization", "Bearer YOUR_TOKEN");
httpClient.Timeout = TimeSpan.FromMinutes(10);

var store = new HttpZarrStore("https://example.com/data.zarr", httpClient);
await using var reader = await OmeZarrReader.OpenAsync(store);

Navigate HCS Plate structure

var plate = reader.AsPlate();
Console.WriteLine($"Plate: {plate.PlateMetadata.Name}");
Console.WriteLine($"Wells: {plate.Wells.Count}");

// Open well B3, field 0
var well = await plate.OpenWellAsync("B", "3");
var field = await well.OpenFieldAsync(0);
var level = await field.OpenResolutionLevelAsync(0);

// Read a plane from the field
var plane = await level.ReadPlaneAsync(c: 0, z: 0);

Work with labels (segmentation masks)

var image = reader.AsMultiscaleImage();

if (await image.HasLabelsAsync())
{
    var labelGroup = await image.OpenLabelsAsync();
    Console.WriteLine($"Available labels: {string.Join(", ", labelGroup.LabelNames)}");
    
    var cellLabel = await labelGroup.OpenLabelAsync("cells");
    var labelLevel = await cellLabel.OpenResolutionLevelAsync(0);
    
    var labelPlane = await labelLevel.ReadPlaneAsync(t: 0, c: 0, z: 0);
    var labelIds = labelPlane.As1DArray<uint>();  // typically uint32
    
    var uniqueCells = labelIds.Distinct().Count(id => id != 0);
    Console.WriteLine($"Detected {uniqueCells} cells");
}

Architecture

The library is structured in clean, composable layers:

┌─────────────────────────────────────────────────────┐
│ OmeZarrReader (Public API)                          │
├─────────────────────────────────────────────────────┤
│ Node Tree Layer                                      │
│  - MultiscaleNode, PlateNode, WellNode, FieldNode   │
│  - ResolutionLevelNode, LabelNode                   │
├─────────────────────────────────────────────────────┤
│ Coordinate Transform Layer                          │
│  - PhysicalROI ↔ PixelRegion                        │
│  - CoordinateTransformService                       │
├─────────────────────────────────────────────────────┤
│ OME-Zarr Metadata Layer                             │
│  - MultiscaleMetadata, PlateMetadata, etc.          │
│  - OmeAttributesParser                              │
├─────────────────────────────────────────────────────┤
│ Zarr Array/Group Layer                              │
│  - ZarrArray (chunk reading, region extraction)     │
│  - ZarrGroup (tree navigation)                      │
├─────────────────────────────────────────────────────┤
│ Codec Pipeline                                       │
│  - BytesCodec, GzipCodec, ZstdCodec                 │
│  - CodecPipeline (ordered application)              │
├─────────────────────────────────────────────────────┤
│ Store Layer (I/O)                                    │
│  - IZarrStore, LocalFileSystemStore                 │
└─────────────────────────────────────────────────────┘

Design Principles

• Separation of Concerns - Each layer has a single, well-defined responsibility
• No Leaky Abstractions - Zarr layer knows nothing about OME, OME layer knows nothing about I/O
• Async Throughout - All I/O operations are async from the start
• Variable Staging Pattern - Readable code with clear intermediate values
• Testable - Interfaces at key boundaries enable unit testing

Supported Features

Data Types

• uint8, uint16

Compression

• Gzip - Standard compression (via System.IO.Compression)
• Zstandard - High-performance compression (via ZstdSharp.Port)
• Uncompressed - Raw data
• Blosc

OME-Zarr Node Types

• Multiscale Images - Pyramidal resolution levels with coordinate transforms
• Labels - Segmentation masks with color/property metadata
• HCS Plates - Wells, fields, acquisitions
• Label Groups - Multiple label arrays per image

Zarr Versions

• Zarr v2 - .zarray, .zattrs, .zgroup files (widely used by Fiji, napari, OMERO)
• Zarr v3 - Single zarr.json per node (newer spec)
• Automatic version detection and handling

API Overview

Core Classes

OmeZarrReader

Entry point for opening datasets. Auto-detects node type.

await using var reader = await OmeZarrReader.OpenAsync(path);
var root = reader.OpenRoot();  // Auto-dispatch to correct type

// Or strongly-typed access
var image = reader.AsMultiscaleImage();
var plate = reader.AsPlate();
var well = reader.AsWell();

ResolutionLevelNode

Represents a single resolution level in a multiscale pyramid.

var level = await image.OpenResolutionLevelAsync(datasetIndex: 0);

// Properties
long[] shape = level.Shape;          // [t, c, z, y, x]
string dtype = level.DataType;       // "uint16", "float32", etc.
double[] pixelSize = level.GetPixelSize();  // Physical size per pixel

// Reading
var plane = await level.ReadPlaneAsync(t: 0, c: 0, z: 5);
var roi = await level.ReadRegionAsync(physicalROI);
var region = await level.ReadPixelRegionAsync(pixelRegion);

// Writing
await level.WriteRegionAsync(pixelRegion, data);

PlaneResult

Result of reading a 2D plane with convenience extraction methods.

var plane = await level.ReadPlaneAsync(t: 0, c: 0, z: 0);

int width = plane.Width;
int height = plane.Height;

// Extract as typed arrays
ushort[,] pixels2D = plane.As2DArray<ushort>();
ushort[] pixels1D = plane.As1DArray<ushort>();

// Convert to specific formats
byte[] gray8 = plane.ToBytes<ushort>(PixelFormat.Gray8);
byte[] bgra32 = plane.ToBytes<ushort>(PixelFormat.Bgra32);

PhysicalROI and PixelRegion

Coordinate representations for ROI specification.

// Physical coordinates (microns, seconds, etc.)
var physicalROI = new PhysicalROI(
    origin: [0, 0, 5.0, 100.0, 200.0],
    size:   [1, 1, 2.0, 50.0, 50.0]
);

// Pixel coordinates (array indices)
var pixelRegion = new PixelRegion(
    start: [0, 0, 10, 100, 200],
    end:   [1, 1, 12, 150, 250]
);

Examples

Iterate through a Z-stack

var axes = level.Multiscale.Axes;
var zIndex = Array.FindIndex(axes, a => a.Name.Equals("z", StringComparison.OrdinalIgnoreCase));
var numSlices = (int)level.Shape[zIndex];

for (int z = 0; z < numSlices; z++)
{
    var plane = await level.ReadPlaneAsync(t: 0, c: 0, z: z);
    var pixels = plane.As1DArray<ushort>();
    
    double meanIntensity = pixels.Average(p => (double)p);
    Console.WriteLine($"Z={z}: mean intensity = {meanIntensity:F1}");
}

Read all channels as separate planes

var cIndex = Array.FindIndex(axes, a => a.Name.Equals("c", StringComparison.OrdinalIgnoreCase));
var numChannels = (int)level.Shape[cIndex];

var channels = new List<ushort[,]>();
for (int c = 0; c < numChannels; c++)
{
    var plane = await level.ReadPlaneAsync(t: 0, c: c, z: 0);
    channels.Add(plane.As2DArray<ushort>());
}

// Create RGB composite, max projection, etc.

Choose optimal resolution level for display

var levels = await image.OpenAllResolutionLevelsAsync();
double targetMicronsPerPixel = 0.5;

var spatialAxisIndex = 3;  // y axis in t,c,z,y,x
var bestLevel = levels
    .Select((l, i) => (level: l, index: i, pixelSize: l.GetPixelSize()[spatialAxisIndex]))
    .OrderBy(l => Math.Abs(l.pixelSize - targetMicronsPerPixel))
    .First();

Console.WriteLine($"Using level {bestLevel.index} ({bestLevel.pixelSize:G4} µm/px)");

Process an entire HCS plate

var plate = reader.AsPlate();

foreach (var wellRef in plate.Wells)
{
    var well = await plate.OpenWellAsync(wellRef.Path);
    
    foreach (var fieldRef in well.Fields)
    {
        var field = await well.OpenFieldAsync(fieldRef.Path);
        var level = await field.OpenResolutionLevelAsync(0);
        
        // Process each field
        var plane = await level.ReadPlaneAsync(c: 0, z: 0);
        // ... analyze, segment, etc.
    }
}

Save plane as image file (using ImageSharp)

using SixLabors.ImageSharp;
using SixLabors.ImageSharp.PixelFormats;

var plane = await level.ReadPlaneAsync(t: 0, c: 0, z: 5);
byte[] pixels = plane.ToBytes<ushort>(PixelFormat.Gray8);

var img = Image.LoadPixelData<L8>(pixels, plane.Width, plane.Height);
img.SaveAsPng("output.png");

Performance Considerations

Chunk-Aligned Reads

For best performance, align ROI boundaries to chunk boundaries when possible:

var chunkShape = level.ZarrArray.Metadata.ChunkShape;  // e.g., [1, 1, 1, 96, 96]

// Good: aligned to chunk boundaries (multiples of 96)
var alignedROI = new PixelRegion(
    start: [0, 0, 0, 0, 0],
    end:   [1, 1, 1, 96, 192]  // 1x2 chunks
);

// Less efficient: crosses chunk boundaries
var unalignedROI = new PixelRegion(
    start: [0, 0, 0, 50, 50],
    end:   [1, 1, 1, 150, 150]  // touches 4 chunks
);

Resolution Level Selection

Use lower resolution levels for overview/navigation, full resolution for analysis:

// Level 0: Full resolution (slow, detailed)
// Level 3: 1/8 resolution (fast, overview)
var overview = await image.OpenResolutionLevelAsync(datasetIndex: 3);
var fullRes = await image.OpenResolutionLevelAsync(datasetIndex: 0);

Memory Management

For large datasets, process in tiles rather than loading entire planes:

int tileSize = 512;
for (int y = 0; y < height; y += tileSize)
{
    for (int x = 0; x < width; x += tileSize)
    {
        var tileRegion = new PixelRegion(
            start: [0, 0, 0, y, x],
            end:   [1, 1, 1, Math.Min(y + tileSize, height), Math.Min(x + tileSize, width)]
        );
        
        var tile = await level.ReadPixelRegionAsync(tileRegion);
        // Process tile...
    }
}

Limitations

• Sharded Zarr v3 - Not yet supported (planned).
• HTTP store listing - ListChildNamesAsync() not supported for HTTP stores. Use explicit path navigation.
• Write support to HTTP - Read-only for remote stores. Use LocalFileSystemStore for writing.
• Full dataset creation - Basic region writing works, but no complete writer API yet.

Roadmap

• HTTP/S3 remote store support
• Blosc codec support
• AWS S3 native SDK integration (ListObjects, credentials)
• Sharded Zarr v3 support
• OME-Zarr writer API for creating new datasets
• Parallel chunk reading for improved performance
• Zarr v2 → v3 conversion utilities
• NGFF transformations support (rotation, affine)
• Consolidated metadata (.zmetadata) support for HTTP stores

Contributing

Contributions welcome! Please:

1. Follow the existing code style (variable staging pattern, clear separation of concerns)
2. Add tests for new features
3. Update documentation
4. Open an issue first for major changes

License

• GNU GPL 3.0 only.

Acknowledgments

• OME-Zarr Specification - https://ngff.openmicroscopy.org/
• Zarr Specification - https://zarr-specs.readthedocs.io/
• ZstdSharp - Managed Zstandard compression
• Inspired by zarr-python, ome-zarr-py, and the broader scientific imaging community

Support

Please use image.sc forum for discussion.

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