update docs index

Co-authored-by: Charlotte Soneson <[email protected]>
Co-authored-by: Michael Stadler <[email protected]>

docs/index.md

@@ -1,4 +1,10 @@
-# Welcome to `ez_zarr`
+<img src="ez_zarr.png" align="right" alt="ez-zarr" width="150"/>
+
+<br>
+
+# Welcome to ez_zarr
+
+<br>
 
 ## Goals
 The aim of `ez_zarr` is to provide easy, high-level access
@@ -11,6 +17,10 @@ The goal is that users can write simple scripts working with plates,
 wells and fields of view, without having to understand how these
 are represented within an OME-Zarr fileset.
 
+In addition to the python package, we also provide an R package
+that automatically generates and wraps a python environment with
+`ez_zarr` and all dependencies, available at https://github.com/fmicompbio/ezzarr.
+
 ## Example
 You can use `ez_zarr` from the command line to get information about an OME-Zarr fileset:
 ```
@@ -33,13 +43,31 @@ img
 #   full_resolution_zyx_spacing (micrometer): [1.0, 0.1625, 0.1625]
 #   segmentations: organoids
 #   tables (measurements): FOV_ROI_table
+
+## legacy objects from `hcs_wrappers`
+from ez_zarr import hcs_wrappers
+
+plate_3d = hcs_wrappers.FractalZarr('tests/example_data/plate_ones.zarr')
+plate_3d
+# FractalZarr plate_ones.zarr
+#   path: tests/example_data/plate_ones.zarr
+#   n_wells: 1
+#   n_channels: 2 (some-label-1, some-label-2)
+#   n_pyramid_levels: 3
+#   pyramid_zyx_scalefactor: {'0': array([1. 2. 2.])}
+#   full_resolution_zyx_spacing: [1.0, 0.1625, 0.1625]
+#   segmentations: 
+#   tables (measurements): FOV_ROI_table
+
 ```
 
 A more extensive example is available from [here](https://fmicompbio.github.io/ez_zarr/getting_started_Image/), also available as an [ipynb notebook](https://fmicompbio.github.io/ez_zarr/getting_started_Image.ipynb).
 
 ## Install
-
-`ez_zarr` is hosted on GitHub at [github.com/fmicompbio/ez_zarr](https://github.com/fmicompbio/ez_zarr) and the documentation can be found at [fmicompbio.github.io/ez_zarr](https://fmicompbio.github.io/ez_zarr/).
+### Using `pip`
+[![PyPI - Version](https://img.shields.io/pypi/v/ez-zarr.svg?logo=pypi&label=PyPI&logoColor=gold)](https://pypi.org/project/ez-zarr/)
+[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/ez-zarr.svg?logo=python&label=Python&logoColor=gold)](https://pypi.org/project/ez-zarr/)
+![PyPI - Downloads](https://img.shields.io/pypi/dm/ez-zarr)
 
 The release version of `ez_zarr` can be installed using pip:
 ```
@@ -51,7 +79,12 @@ The current (development) version of `ez_zarr` can be installed from github.com
 pip install git+ssh://[email protected]/fmicompbio/ez_zarr.git
 ```
 
-Alternatively, you can install `ez_zarr` using conda from the `conda-forge` channel by:
+### Using `conda`
+[![Conda Version](https://img.shields.io/conda/vn/conda-forge/ez-zarr.svg)](https://anaconda.org/conda-forge/ez-zarr)
+[![Conda Platforms](https://img.shields.io/conda/pn/conda-forge/ez-zarr.svg)](https://anaconda.org/conda-forge/ez-zarr)
+[![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/ez-zarr.svg)](https://anaconda.org/conda-forge/ez-zarr)
+
+Alternatively, you can install `ez-zarr` from the `conda-forge` channel using:
 ```
 conda install -c conda-forge --override-channels ez-zarr
 ```
@@ -66,4 +99,18 @@ is with the Friedrich Miescher Insitute for Biomedical Research
 (see [LICENSE](https://github.com/fmicompbio/ez_zarr/blob/main/LICENSE)).
 
 `ez_zarr` is being developed at the Friedrich Miescher Institute for
-Biomedical Research by [@silvbarb](https://github.com/silvbarb), [@csoneson](https://github.com/csoneson) and [@mbstadler](https://github.com/mbstadler).
+Biomedical Research by [@silvbarb](https://github.com/silvbarb), [@csoneson](https://github.com/csoneson) and [@mbstadler](https://github.com/mbstadler).
+
+## Need help? 
+If you run into problems when using `ez_zarr`, please first check whether the 
+answer is available in the [help pages for the individual functions underneath 'Documentation'](https://fmicompbio.github.io/ez_zarr/) or in 
+the ['Getting started' vignette](https://fmicompbio.github.io/ez_zarr/getting_started_Image/).
+If not, please [open an issue](https://github.com/fmicompbio/ez_zarr/issues/new) 
+and explain your problem. Try to provide a reproducible example, and always 
+include the code you used, that will make it much easier for us to help.
+
+## Contributions
+If you would like to contribute to `ez_zarr`, you can do so by sending a pull 
+request to this repository. If the contribution involves changes in the 
+functionality provided by `ez_zarr`, we encourage you to first open an issue 
+to discuss the intended contribution.