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axtimwalde authored Oct 11, 2024
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A Fiji plugin for loading and saving image data to N5 containers. Supports [HDF5](https://www.hdfgroup.org/solutions/hdf5/), [Zarr](https://zarr.readthedocs.io/en/stable/#), [Amazon S3](https://aws.amazon.com/s3/), and [Google cloud storage](https://cloud.google.com/storage).

## Contents
1. [Open N5](#open-n5)
1. [Open HDF5/N5/Zarr/OME-NGFF](#open-n5)
1. [Virtual](#virtual)
2. [Cropping](#cropping)
2. [Export N5](#export-n5)
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6. [Details](#details)
1. [Cloud writing benchmarks](#cloud-writing-benchmarks)

## Open N5
## Open HDF5/N5/Zarr/OME-NGFF

Open N5 datasets from Fiji with `File > Import > HDF5/N5/Zarr/OME-NGFF ... `.
Open HDF5/N5/Zarr/OME-NGFF datasets from Fiji with `File > Import > HDF5/N5/Zarr/OME-NGFF ... `.

Quickly open a dataset by pasting the full path to the dataset and press `OK`.
For example, try `gs://example_multi-n5_bucket/mitosis.n5/raw` to open the sample mitosis image from Google
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### Virtual

Check the `Open as virtual` box to open the n5 dataset as a [virtual stack in ImageJ](https://imagej.nih.gov/ij/docs/guide/146-8.html#toc-Section-8).
Check the `Open as virtual` box to open the dataset as a [virtual stack in ImageJ](https://imagej.nih.gov/ij/docs/guide/146-8.html#toc-Section-8).
This enable the opening and viewing of image data that do not fit in RAM. Image slices are loaded on-the-fly, so
navigation will be slow when parts of the images are loaded.

### Cropping

Subsets of images can be opened by checking the `Crop` box in the dialog, then pressing `OK`.
Subsets of datasets can be opened by checking the `Crop` box in the dialog, then pressing `OK`.
A separate dialog will appear for each selected dataset as shown below.

<img src=https://raw.githubusercontent.com/saalfeldlab/n5-ij/master/doc/OpenN5DialogWithCrop.png width="700">
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subset. The opened interval includes both min and max values, so the image will be of size `max - min + 1` along
each dimension. In the example shown above, the resulting image will be of size `101 x 111 x 2 x 51`.

## Export N5
## Export HDF5/N5/Zarr/OME-NGFF

Save images opened in Fiji as N5 datasets with `File > Save As > Export N5`.
Save images opened in Fiji as HDF5/N5/Zarr/OME-NGFF datasets with `File > Save As > Export HDF5/N5/Zarr/OME-NGFF ...`.

<img src=https://raw.githubusercontent.com/saalfeldlab/n5-ij/master/doc/SaveN5Dialog.png width="280">

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* HDF5
* Specify a file ending in `.h5` ,`.hdf5`, or `.hdf`
* example `C:\user\docs\example.h5`

## Backend

Specify the backend by protocol, "file:" or not protocol indicate the local file system:

* Amazon S3
* Specify one of two url styles:
* `s3://bucket-name/path/to/root.n5`
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1) ImageJ-style metadata
2) [N5-viewer](https://github.com/saalfeldlab/n5-viewer) metadata
3) [COSEM](https://github.com/janelia-cosem/schemas/blob/master/multiscale.md) metadata
4) Custom metadata. [Read details here](CustomMetadata.md)
4) [OME-NGFF](https://ngff.openmicroscopy.org/latest/) metadata
5) Custom metadata. [Read details here](CustomMetadata.md)

The metadata style for exported N5 datasets is customizable, more detail coming soon.
The metadata style for exported HDF5/N5/Zarr/OME-NGFF datasets is customizable, more detail coming soon.

## For developers

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