Modern Imaging Format Support

Fileglancer automatically detects modern imaging formats (OME-Zarr and N5) when you navigate into a compatible directory.

Zarr / OME-Zarr Support

Zarr preview panel

The Zarr preview panel shows a metadata table, thumbnail preview, and “Open with” buttons for compatible viewers for Zarr datasets.

Thumbnail previews are only generated for OME-Zarr datasets, and only if the first multiscale level is small enough to generate a thumbnail.

The metadata table includes:

• Zarr Version (v2, v3, or both if markers for multiple versions are present)
• Content (auto-detected) — heuristical image vs. segmentation detection (can be enabled/disabled in preferences)
• Data Type (e.g., uint8, float32)
• Shape and Chunk Size (for plain arrays)
• Multiscale Levels (for OME-Zarr)
• Labels (if a labels sub-directory is present)
• Per-axis details: axis name, shape, chunk size, scale, and unit

When the Zarr preview panel appears

The Zarr preview panel appears when Fileglancer detects Zarr marker files in the current directory. The presence of these files indicates that the directory contains Zarr data:

• Zarr v2: .zarray (plain array) or .zattrs (OME-Zarr group)
• Zarr v3: zarr.json

For the dataset to be recognized as OME-Zarr and show the full preview panel with metadata and viewer options, the following conditions must be met:

• For a Zarr v2 group, the .zattrs file must contain a multiscales field to be recognized as OME-Zarr.
• For a Zarr v3 group, the zarr.json file must contain attributes.ome.multiscales to be recognized as OME-Zarr.

Zarr data links for Neuroglancer

For Neuroglancer to open a Zarr dataset, the dataset must be:s

1. organized in the way Neuroglancer expects (e.g., OME-Zarr or plain Zarr array with appropriate metadata), and
2. accessible via an HTTP URL.

In Fileglancer, this means creating a data link for the directory that shows a Zarr or N5 preview panel. A data link is a proxied URL that makes the dataset accessible over the network.

• If a data link already exists, the Neuroglancer button is immediately active.
• If no data link exists, clicking the Neuroglancer button prompts you to create one.

OME-Zarr datasets (with multiscales) support all available viewers: Neuroglancer, Vol-E, Avivator (v2 only), and the OME-ZARR Validator.

Plain Zarr arrays (without multiscales) only support Neuroglancer.

Zarr data links for other viewers

Data links can also be used to open OME-Zarr datasets in other compatible viewers. Viewers that are integrated into Fileglancer are detailed in Integrated Data Tools below, but data links can be used with any viewer that supports loading data via an HTTP URL.

N5 Support

N5 metadata table

The N5 preview panel reads metadata from attributes.json (root) and s0/attributes.json (first scale level) and displays:

• N5 Version (from the n5 field in attributes.json)
• Data Type (from s0/attributes.json, e.g., uint16)
• Dimensions (from s0/attributes.json)
• Block Size (from s0/attributes.json)
• Multiscale Levels (from downsamplingFactors or scales in attributes.json)
• Compression (type and level, from s0/attributes.json)
• Per-axis details: axis name, shape, resolution, and unit

When the N5 preview panel appears

Fileglancer shows the N5 preview panel when it detects both of these inside the current directory:

1. An attributes.json file (the root N5 metadata)
2. An s0/ subdirectory (the first scale level)

Missing metadata warnings

The N5 metadata table highlights missing fields that affect how viewers interpret the data:

• No resolution: If neither resolution nor pixelResolution.dimensions is found in attributes.json, resolution is shown as “Unknown” with a warning: “No ‘resolution’ or ‘pixelResolution.dimensions’ found in attributes.json. Neuroglancer uses these to define the physical scale of each dimension.”
• No units: If neither units nor pixelResolution.unit is found in attributes.json, the unit column is blank with a warning: “No ‘units’ or ‘pixelResolution.unit’ found in attributes.json. Viewers may assume a default unit when none is specified.”
• No downsampling factors: If neither downsamplingFactors nor scales is found in attributes.json, multiscale levels shows “Not specified” with a warning: “No ‘downsamplingFactors’ or ‘scales’ found in attributes.json. Neuroglancer can also read ‘downsamplingFactors’ from individual sN/attributes.json files.”

N5 data links for Neuroglancer

Like Zarr, N5 datasets require a data link for the directory that shows an N5 preview panel. Neuroglancer is the only integrated viewer for N5 datasets, but data links can be used with other viewers that support loading data via a HTTP URL.

Integrated Data Tools

Several web-based viewers and tools for OME-Zarr and N5 datasets are directly integrated into Fileglancer. When you open a compatible dataset, “Open with” buttons appear in the preview panel to launch these tools directly from Fileglancer.

Neuroglancer

• A powerful web-based viewer for large-scale volumetric data.
• Supported formats: OME-Zarr, plain Zarr arrays, N5

Vol-E (Volume Explorer)

• Allen Cell Institute’s volume viewer designed for cellular and subcellular imaging.
• Supported formats: OME-Zarr only

Avivator

• A lightweight, web-based image viewer for OME-Zarr data.
• Supported formats: OME-Zarr v2 only

OME-ZARR Validator

• A diagnostic tool for verifying OME-Zarr datasets against the OME-Zarr specification.
• Supported formats: OME-Zarr only

Accessing Data Tools from Fileglancer

Locating Tool Options

When you navigate to a compatible dataset (OME-Zarr, Zarr, or N5 format):

1. View the file/directory in Fileglancer
   Navigate to your dataset directory. The dataset will be recognized automatically if it meets the Zarr or N5 criteria, and the preview panel will appear above the file list.

2. Find the “Open with” section
   Located in the file preview area, below the thumbnail preview of the dataset, there is a list of compatible viewers with their respective logos. There is also a button to copy the direct data link.

Launching Viewers

1. Click the desired viewer button Each viewer opens in a new browser tab once a data link is available.

2. Share viewer URLs Copy the URL from the opened viewer tab. Share with internal collaborators. URLs remain valid as long as data links are active.

Troubleshooting

Preview Panel Not Appearing

For Zarr directories:

• Verify the directory contains at least one Zarr marker file: zarr.json, .zarray, or .zattrs
• For OME-Zarr, ensure the metadata includes a multiscales field

For N5 directories:

• Verify the directory contains both attributes.json and an s0/ subdirectory
• Ensure s0/attributes.json exists and is readable

Data Loading Issues

Problem: A tool opens but no data appears

• Verify data format compatibility
• Ensure data structure is correct
• Request conversion to compatible format

Performance Issues

Problem: Slow data loading

• Check data chunk sizes and compression
• Consider creating optimized versions for viewing
• Verify network connectivity and speed

Sharing Issues

Problem: Shared URLs don’t work for collaborators

• Check the data link is still active
• Ensure collaborators are on correct network