Adds interactive image to main docs page

index.rst → 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:
+
+<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>
+
+You can find more samples of such data from the Image Data Resource at <https://idr.github.io/ome-ngff-samples/>.
+
+## 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 <https://www.openmicroscopy.org/>`_, 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 </specifications/index.html>`_!
+   * [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 <https://bff.allencell.org/datasets>`_
+- [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>`_
+- [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 </tools/index.html>`_!
+   * Check out the [tools section](/tools/index.html)!
 * Want to create a Zarr?
-   * Check out the `tools section </tools/index.html>`_!
+   * Check out the [tools section](/tools/index.html)!
 * Want to see or download a Zarr?
-   * Check out the `data section </data/index.html>`_!
+   * 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
+```