.. NGFF documentation master file, created by
   sphinx-quickstart on Tue Mar 14 08:54:12 2023.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Next-Generation File Formats (NGFF) + OME-Zarr
===============================================

Welcome to the Next-Generation File Formats (NGFF) main page! This site is dedicated to providing resources for the NGFF community and those that are interested in getting started with OME-Zarr.

NGFF vs OME-Zarr, what is the difference?
------------------------------------------
**OME-Zarr** is the file format that the NGFF community has settled on to address issues of scalability and interoperability described below.

**NGFF** is the community-driven process for designing the next generation of bioimaging formats. NGFF brings together the community to define shared specifications, metadata standards, and best practices. OME-Zarr implements those decisions, providing a practical, open, and scalable way to store and share modern microscopy data. As the NGFF specifications evolve, OME-Zarr evolves with them — ensuring the format reflects the needs and experience of the wider community.

What is an OME-Zarr?
------------------------
An OME-Zarr is a file format optimized for storying, viewing, & sharing large images.
There are two parts to an OME-Zarr:

* **The "Zarr" part describes how the pixel data for the images are laid out**
* The "OME", which stands for `Open Microscopy Environment <https://www.openmicroscopy.org/>`_, part describes metadata about the pixel data. This includes metadata such as:
   * spatial relationships
   * high content screening data
   * well data
   * `and more </specifications/index.html>`_!

Why would I use OME-Zarr?
--------------------------
OME-Zarr files have two major benefits:

* Chunking is inherent to "Zarr" files. This means "Zarr" files are stored in independently-accessible blocks.
   * **Storage**: Microscopy images can be quite large and can therefore reach Cloud system storage limits for individual files; the chunked nature of a Zarr can alleviate this issue. Some storage systems may also duplicate byte-equivalent files, so a chunked file like Zarr may save storage space.
   * **Viewing**: Viewers can target specific chunks to load based upon the current view, reducing lag, & enabling massive images to be viewed within browsers.
   * **Cost**: When viewing or reading data, the total cost of accessing a Zarr file on the cloud may be less than a more monolithic file format due to the more efficient data access patterns. Ex. A viewer can just access the chunks of the image it needs to display rather than the entire image.
* "OME-Zarr" is a "Zarr" with embedded standardized metadata in the Open Microscopy Environment (OME) format.
   * **Sharing**: A standardized imaging metadata format can ease cross-organization file sharing and can therefore aid organizational collaboration and data sharing.
   * **Interoperability**: Standardized metadata can also enable the interoperability of tools.

When would I not use OME-Zarr?
------------------------------
* If your file isn’t very big and you’re working with local data, the current specification of OME-Zarr can be less convenient than a single-file format and the benefits are limited. Planned expansions to the OME-Zarr specification will make it more convenient to work with it in these scenarios (e.g. single-file Zarrs) and add features that might make it beneficial to use OME-Zarr even in these scenarios (e.g. transformations).
* If your original file is lossy compressed, you will see a large increase in file size as the images are decompressed into OME-Zarr. There is not yet support for transferring lossy compressed image tiles to OME-Zarr. This currently impacts most whole slide image (WSI) formats such as SVS, CZI, and NDPI, which are lossy JPEG compressed by default and see about a 10x size increase into OME-Zarr.

Who is using OME-Zarr?
-----------------------

These are *some* of the organizations (and their dataset pages) that are using OME-Zarr for their data.

- `Allen Institute <https://bff.allencell.org/datasets>`_
- biohub
- `Broad Institute <https://broadinstitute.github.io/cellpainting-gallery/overview.html>`_
- `EMBL - Image Data Resource (IDR) <https://idr.openmicroscopy.org/>`_
- `Howard Hughes Medical Institute, Janelia (HHMI) <https://openorganelle.janelia.org/>`_
- `Jackson Laboratory (JAX) <https://images.jax.org/>`_
- ... `and more </data/index.html>`_

How do I use OME-Zarr?
----------------------

* Already have a Zarr?
   * Check out the `tools section </tools/index.html>`_!
* Want to create a Zarr?
   * Check out the `tools section </tools/index.html>`_!
* Want to see or download a Zarr?
   * Check out the `data section </data/index.html>`_!

Have other questions?
======================
Check out the pages below, including the FAQ page.

.. toctree::
   :maxdepth: 1

   community/index
   contributing/index
   specifications/index
   rfc/index
   resources/index
   help-desk/index