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docs-connecting-missing-links #35

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Nov 7, 2021
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4 changes: 2 additions & 2 deletions docs/source/contact_us/github.rst
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Expand Up @@ -3,10 +3,10 @@ Report a bug/Request a feature
================================

If you like to report a bug/request a feature/communicate any related problem
best way to reach us creating a new issue on our [GitHub repository]().
best way to reach us creating a new issue on our `GitHub repository <https://github.com/royerlab/aydin>`_.

You can also track pull-requests, milestones and our plans on our repository.
Feel free to participate in discussions and contribute but do not forget to
read our [contributing guidelines] first.
read our `contributing guidelines <https://github.com/royerlab/aydin/blob/master/CONTRIBUTING.md>`_ first.


6 changes: 3 additions & 3 deletions docs/source/getting_started/install.rst
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Expand Up @@ -20,7 +20,7 @@ Aydin on your computer.
Install Aydin bundle on Mac OSX
---------------------------------------

Download the `OSX bundle <http://www.google.com/>`_ to start. Then right-click and open the Aydin installer as shown
Download the `OSX bundle <https://royerlab.github.io/aydin/>`_ to start. Then right-click and open the Aydin installer as shown
below:

.. image:: ../resources/install/osx/right_click_open.png
Expand Down Expand Up @@ -61,7 +61,7 @@ folder as shown below:
Install Aydin bundle on Windows
---------------------------------------

Download the `Windows bundle <http://www.google.com/>`_ to start. Then extract the compressed
Download the `Windows bundle <https://royerlab.github.io/aydin/>`_ to start. Then extract the compressed
Aydin bundle, you should be able to see the see extracted folder as shown
below:

Expand All @@ -77,7 +77,7 @@ You can open the folder and double-click on the ``run-aydin`` file to start Aydi
Install Aydin bundle on Linux
---------------------------------------

Download the `Linux bundle <http://www.google.com/>`_ to start. Then extract the Aydin bundle
Download the `Linux bundle <https://royerlab.github.io/aydin/>`_ to start. Then extract the Aydin bundle
from the compressed file. You should be able to see the see extracted folder as shown below:

.. image:: ../resources/install/linux/unzip_bundle.png
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12 changes: 8 additions & 4 deletions docs/source/index.rst
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Expand Up @@ -11,9 +11,11 @@ a number of self-supervised, auto-tuned, and unsupervised image denoising algori
Aydin handles from the get-go n-dimensional array-structured images with an arbitrary number
of batch dimensions, channel dimensions, and typically up to 4 spatio-temporal dimensions.

It comes with `Aydin Studio` a [graphical user interface]
It comes with `Aydin Studio` a `graphical user interface <https://royerlab.github.io/aydin/tutorials/gui_tutorials.html>`_
to easily experiment with all the different algorithms and parameters available,
a [command line interface] to run large jobs offline, and an [API] for
a `command line interface <https://royerlab.github.io/aydin/tutorials/cli_tutorials.html>`_
to run large jobs offline, and an
`API <https://royerlab.github.io/aydin/api/introduction.html>`_ for
custom coding and integration into other packages.

Getting started, with bundles:
Expand Down Expand Up @@ -51,10 +53,12 @@ profiles, some of our best algorithms can easily run on modest machines.

Documentation
~~~~~~~~~~~~~~
Tutorials can be found [here] for an exhaustive tour of features and parameters for both
Tutorials can be found `here <https://royerlab.github.io/aydin/tutorials/tutorials_home.html>`_
for an exhaustive tour of features and parameters for both
the graphical interface (Aydin Studio), command line interface (CLI), and
Python programming interface (API). To better understand how to tune parameters
for a given image, please check our [use cases] where we go through.
for a given image, please check our `use cases <https://royerlab.github.io/aydin/use_cases/introduction.html>`_
where we go through.

How to cite?
~~~~~~~~~~~~~
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