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Merge pull request #483 from lubianat/images_on_page
Adds interactive image to main docs page
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.. NGFF documentation master file, created by
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sphinx-quickstart on Tue Mar 14 08:54:12 2023.
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You can adapt this file completely to your liking, but it should at least
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contain the root `toctree` directive.
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Next-Generation File Formats (NGFF) + OME-Zarr
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===============================================
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# Next-Generation File Formats (NGFF) + OME-Zarr
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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.
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NGFF vs OME-Zarr, what is the difference?
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------------------------------------------
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In summary, OME-Zarr allows you to store, share and stream large images like these 500 GB:
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<iframe style="width: 100%; height: 500px" name="vizarr" src="https://hms-dbmi.github.io/vizarr/?source=https://livingobjects.ebi.ac.uk/idr/zarr/v0.1/4495402.zarr"></iframe>
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You can find more samples of such data from the Image Data Resource at <https://idr.github.io/ome-ngff-samples/>.
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## NGFF vs OME-Zarr, what is the difference?
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**OME-Zarr** is the file format that the NGFF community has settled on to address issues of scalability and interoperability described below.
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**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.
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What is an OME-Zarr?
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------------------------
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## What is an OME-Zarr?
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An OME-Zarr is a file format optimized for storying, viewing, & sharing large images.
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There are two parts to an OME-Zarr:
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* **The "Zarr" part describes how the pixel data for the images are laid out**
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* The "OME", which stands for `Open Microscopy Environment <https://www.openmicroscopy.org/>`_, part describes metadata about the pixel data. This includes metadata such as:
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* The "OME", which stands for [Open Microscopy Environment](https://www.openmicroscopy.org/), part describes metadata about the pixel data. This includes metadata such as:
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* spatial relationships
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* high content screening data
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* well data
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* `and more </specifications/index.html>`_!
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* [and more](/specifications/index.html)!
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## Why would I use OME-Zarr?
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Why would I use OME-Zarr?
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--------------------------
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OME-Zarr files have two major benefits:
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* Chunking is inherent to "Zarr" files. This means "Zarr" files are stored in independently-accessible blocks.
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* **Sharing**: A standardized imaging metadata format can ease cross-organization file sharing and can therefore aid organizational collaboration and data sharing.
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* **Interoperability**: Standardized metadata can also enable the interoperability of tools.
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When would I not use OME-Zarr?
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------------------------------
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* 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).
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## When would I not use OME-Zarr?
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* 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).
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* 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.
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Who is using OME-Zarr?
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-----------------------
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## Who is using OME-Zarr?
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These are *some* of the organizations (and their dataset pages) that are using OME-Zarr for their data.
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- `Allen Institute <https://bff.allencell.org/datasets>`_
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- [Allen Institute](https://bff.allencell.org/datasets)
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- biohub
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- `Broad Institute <https://broadinstitute.github.io/cellpainting-gallery/overview.html>`_
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- `EMBL - Image Data Resource (IDR) <https://idr.openmicroscopy.org/>`_
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- `Howard Hughes Medical Institute, Janelia (HHMI) <https://openorganelle.janelia.org/>`_
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- `Jackson Laboratory (JAX) <https://images.jax.org/>`_
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- ... `and more </data/index.html>`_
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- [Broad Institute](https://broadinstitute.github.io/cellpainting-gallery/overview.html)
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- [EMBL - Image Data Resource (IDR)](https://idr.openmicroscopy.org/)
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- [Howard Hughes Medical Institute, Janelia (HHMI)](https://openorganelle.janelia.org/)
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- [Jackson Laboratory (JAX)](https://images.jax.org/)
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- ... [and more](/data/index.html)
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How do I use OME-Zarr?
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----------------------
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## How do I use OME-Zarr?
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* Already have a Zarr?
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* Check out the `tools section </tools/index.html>`_!
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* Check out the [tools section](/tools/index.html)!
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* Want to create a Zarr?
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* Check out the `tools section </tools/index.html>`_!
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* Check out the [tools section](/tools/index.html)!
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* Want to see or download a Zarr?
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* Check out the `data section </data/index.html>`_!
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* Check out the [data section](/data/index.html)!
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## Have other questions?
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Have other questions?
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======================
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Check out the pages below, including the FAQ page.
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Check out the pages below, including the [FAQ](help-desk/index.md#faqs) page.
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.. toctree::
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:maxdepth: 1
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```{toctree}
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:maxdepth: 1
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community/index
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contributing/index
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specifications/index
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rfc/index
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resources/index
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help-desk/index
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community/index
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contributing/index
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specifications/index
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rfc/index
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resources/index
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help-desk/index
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```

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