diff --git a/index.rst b/index.md similarity index 58% rename from index.rst rename to index.md index 87f98687..8f213cf0 100644 --- a/index.rst +++ b/index.md @@ -1,33 +1,33 @@ -.. 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 -=============================================== +# 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? ------------------------------------------- +In summary, OME-Zarr allows you to store, share and stream large images like these 500 GB: + + + +You can find more samples of such data from the Image Data Resource at . + +## 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? ------------------------- +## 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 `_, part describes metadata about the pixel data. This includes metadata such as: +* 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 `_! + * [and more](/specifications/index.html)! + +## Why would I use OME-Zarr? -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. @@ -38,44 +38,43 @@ OME-Zarr files have two major benefits: * **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). +## 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? ------------------------ +## 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 `_ +- [Allen Institute](https://bff.allencell.org/datasets) - biohub -- `Broad Institute `_ -- `EMBL - Image Data Resource (IDR) `_ -- `Howard Hughes Medical Institute, Janelia (HHMI) `_ -- `Jackson Laboratory (JAX) `_ -- ... `and more `_ +- [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? ----------------------- +## How do I use OME-Zarr? * Already have a Zarr? - * Check out the `tools section `_! + * Check out the [tools section](/tools/index.html)! * Want to create a Zarr? - * Check out the `tools section `_! + * Check out the [tools section](/tools/index.html)! * Want to see or download a Zarr? - * Check out the `data section `_! + * Check out the [data section](/data/index.html)! + +## Have other questions? -Have other questions? -====================== -Check out the pages below, including the FAQ page. +Check out the pages below, including the [FAQ](help-desk/index.md#faqs) page. -.. toctree:: - :maxdepth: 1 +```{toctree} +:maxdepth: 1 - community/index - contributing/index - specifications/index - rfc/index - resources/index - help-desk/index +community/index +contributing/index +specifications/index +rfc/index +resources/index +help-desk/index +```