Update Getting Started (#287)

* remove numbers and update version

* bold headline in rst

* copyedited for clarity and  correctness

* fix formatting

* change dev content to note

* change formatting in Usage

* update license badge with correct target

* update README cmd version to 1.1.0

* crop images to be the same size

README.md

@@ -2,7 +2,7 @@
 
 [![Build Status](https://travis-ci.com/vanvalenlab/kiosk.svg?branch=master)](https://travis-ci.com/vanvalenlab/kiosk)
 [![Read the Docs](https://img.shields.io/readthedocs/kiosk?logo=Read%20the%20Docs)](https://deepcell-kiosk.readthedocs.io/en/master)
-[![Apache 2.0](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+[![Apache 2.0](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://github.com/vanvalenlab/kiosk/blob/master/LICENSE)
 
 The DeepCell Kiosk is the entry point for users to spin up an end-to-end DeepCell environment in the cloud using [Kubernetes](https://kubernetes.io/). It is designed to allow researchers to easily deploy and scale a deep learning platform for biological image analysis. Once launched, users can drag-and-drop images to be processed in parallel using publicly available, or custom-built, TensorFlow models. To train custom models, please refer to [DeepCell-TF](https://github.com/vanvalenlab/deepcell-tf), which was designed to facilitate model development and export these models for use with the DeepCell Kiosk.
 
@@ -46,7 +46,7 @@ Tracked Image
 Start a terminal shell and install the DeepCell Kiosk wrapper script:
 
 ```bash
-docker run -e DOCKER_TAG=1.0.0 vanvalenlab/kiosk:1.0.0 | sudo bash
+docker run -e DOCKER_TAG=1.1.0 vanvalenlab/kiosk:1.1.0 | sudo bash
 ```
 
 To start the kiosk, just run `kiosk` from the terminal shell.
@@ -84,7 +84,7 @@ A [FAQ](http://www.deepcell.org.faq) page is also available.
 
 ## License
 
-This software is license under a modified [APACHE2](https://opensource.org/licenses/Apache-2.0). See [LICENSE](https://github.com/vanvalenlab/kiosk/blob/master/LICENSE) for full  details.
+This software is license under a modified [APACHE2](https://opensource.org/licenses/Apache-2.0). See [LICENSE](https://github.com/vanvalenlab/kiosk/blob/master/LICENSE) for full details.
 
 ## Trademarks
 

docs/source/GETTING_STARTED.rst

@@ -12,9 +12,9 @@ Getting Started
 Google Cloud Setup
 ------------------
 
-.. warning:: Google Cloud Platform must approve several requests which may take up to 1 day to complete.
+.. warning:: Google Cloud Platform must approve several requests that may take up to 1 day to complete.
 
-1. If necessary, create an account at `Google Cloud <https://cloud.google.com>`_ and create a Google Cloud project, making sure you have at least one account with the `Owner` role. Write down the project ID (you will need this in step 9).
+1. If necessary, create an account at `Google Cloud <https://cloud.google.com>`_ and create a Google Cloud project, making sure you have at least one account with the `Owner` role. Take note of the project ID (you will need this later during Kiosk configuration).
 
 2. Make sure the `Kubernetes Engine API <https://console.cloud.google.com/apis/api/container.googleapis.com/overview>`_ is enabled.
 
@@ -26,7 +26,7 @@ Google Cloud Setup
 
 .. note:: Google offers a number of GPU types. The DeepCell Kiosk uses `nvidia-tesla-t4` GPUs for inference by default.
 
-5. Create a `cloud storage bucket <https://cloud.google.com/storage/docs/creating-buckets>`_. This will be used to store data and models. Record the bucket name (you will need this in step 9). Please do not use underscores (`_`) in your bucket name. Your bucket should follow the organizational structure that follows:
+5. Create a `cloud storage bucket <https://cloud.google.com/storage/docs/creating-buckets>`_. This will be used to store data and models. Record the bucket name (as with project ID, you will need this during Kiosk configuration). Please do not use underscores (`_`) in your bucket name. Your bucket should follow the organizational structure that follows:
 
    .. code-block:: bash
 
@@ -37,7 +37,7 @@ Google Cloud Setup
        |-- uploads
        |-- output
 
-   | ``/models`` can be changed by modifying the ``MODEL_PREFIX`` environmental variable in the ``tf-serving`` helmfile. Similarly, ``/uploads`` can be configured by modifying ``UPLOAD_PREFIX`` in the ``frontend`` helmfile. The contents of ``/uploads`` and ``/output`` are managed by the |kiosk-bucket-monitor|.
+   Please note that the Kiosk comes "preloaded" with a few commonly used models. These models are hosted in our public ``deepcell-models`` bucket on Google Cloud. However, if you wish to use custom models, you can do so by altering the ``GCLOUD_STORAGE_BUCKET`` environmental variable in the ``tf-serving`` helmfile. The contents of ``/uploads`` and ``/output`` are managed by the |kiosk-bucket-monitor|.
 
 .. |kiosk-bucket-monitor| raw:: html
 
@@ -50,10 +50,10 @@ Launching the DeepCell Kiosk
 
 One of the enabling technologies the DeepCell Kiosk utilizes is `Docker <https://www.docker.com/>`_ (*FREE Community Edition*). Installation is easy for Linux and MacOS, but the setup can be complicated for Windows. For this reason, we recommend Windows users employ an `Ubuntu VM <https://brb.nci.nih.gov/seqtools/installUbuntu.html>`_ or follow the cloud jumpbox workflow outlined below.
 
-If you plan on maintaining the DeepCell kiosk as a persistent tool, we recommend using the jumpbox workflow, which allows you to manage the kiosk from a Google Cloud VM. This prevents computer shutdowns from interfering with your ability to manage the kiosk.
+If you plan on maintaining the DeepCell Kiosk as a persistent tool, we recommend using the jumpbox workflow, which allows you to manage the system from a Google Cloud VM. This prevents unexpected or accidental computer shutdowns that occur locally from interfering with your ability to manage the Kiosk.
 
 .. _DOCKER_INSTALLATION:
-6. Select the docker installation that is best for you:
+**Select the docker installation that is best for you:**
 
    * `Local Docker Installation - Windows`_
    * `Local Docker Installation - MacOS and Linux`_
@@ -73,7 +73,7 @@ Cloud-Based Jumpbox Workflow
 * Navigate to the `VM instances <https://console.cloud.google.com/compute/instances>`_ page via ``Compute Engine > VM instances``
 * Check that your boot disk is configured for ``Debian/Ubuntu 9`` operating system
 
-.. warning:: Container optimized images do not support kiosk installation.
+.. warning:: Container optimized images do not support Kiosk installation.
 
 * All other settings can be left as defaults
 * After creating the instance, SSH into your instance either using the option provided by Google Cloud or through your local terminal.
@@ -88,22 +88,20 @@ Cloud-Based Jumpbox Workflow
     sudo apt-get update && \
     sudo apt-get install -y containerd.io docker-ce docker-ce-cli git make vim
 
-* Alternatively, if you SSH'd in using Google Cloud's browser-based terminal, you will need to break that large clump of commands into individual commands (each semicolon denotes the end of a command) and paste them one at a time onto the command line. After this, you should see the kiosk GUI screen and can follow the kiosk configuration and launch process as usual.
-
 Starting the Kiosk
 ^^^^^^^^^^^^^^^^^^
 
-You are now ready to start the kiosk! Those interested in Kiosk development should follow a different path to start the kiosk which is described in :ref:`DEVELOPER`.
+You are now ready to start the Kiosk!
 
-7. Start a terminal shell and install the DeepCell Kiosk wrapper script:
+* Start a terminal shell and install the DeepCell Kiosk wrapper script:
 
 .. code-block:: bash
 
-    docker run -e DOCKER_TAG=1.0.0 vanvalenlab/kiosk:1.0.0 | sudo bash
+    docker run -e DOCKER_TAG=1.1.0 vanvalenlab/kiosk:1.1.0 | sudo bash
 
 .. note:: This command and the one that follows may need to be preceded by `sudo` depending on your permission settings.
 
-8. To start the kiosk, just run ``kiosk`` from the terminal shell
+* To start the Kiosk, just run ``kiosk`` from the terminal shell
 
 .. list-table::
 
@@ -112,17 +110,21 @@ You are now ready to start the kiosk! Those interested in Kiosk development shou
     * - .. image:: ../images/Kiosk-Welcome.png
       - .. image:: ../images/Kiosk-Main-Menu.png
 
+.. note:: Those interested in Kiosk development should follow a different path to start the Kiosk which is described in :ref:`DEVELOPER`.
+
 DeepCell Kiosk Usage
 --------------------
 
-9. Once the Kiosk has started, select the configuration option for your chosen cloud provider (currently, only Google Cloud is supported). The next screen will prompt you to authenticate your account with gcloud or to continue with a previously authenticated account. The next several screens will prompt you to select a gcloud project, name your cluster and finally enter a bucket name for data storage. To complete cluster configuration you have the option to choose between "Default" and "Advanced" configuration. "Default" will set standard values for compute hardware and will be appropriate for most users. "Advanced" allows configure each setting individually.
+* Once the Kiosk has started, select the configuration option for your chosen cloud provider (currently, only Google Cloud is supported). The next screen will prompt you to authenticate your account with gcloud or to continue with a previously authenticated account. The next several screens will prompt you to select a gcloud project, name your cluster, and enter a bucket name for data storage. If you followed the Google Cloud Setup instructions from above, you should use that project and bucket name.
+
+* To complete cluster configuration, you have the option to choose between "Default" and "Advanced" configuration. The "Default" configuration option sets standard values for compute hardware and is appropriate for most users. The "Advanced" option allows users to configure each setting individually.
 
-10. At the completion of configuration, you will return to the home screen where you can select the "Create" option to trigger creation of the cluster based on your configured values. This may take up to 10 minutes. Following successful creation, you will see a confirmation page.
+* Once cluster configuration is complete, you will return to the home screen. There you can select the "Create" option to trigger cluster creation based on your configured values. This may take up to 10 minutes. Following successful creation, you will see a confirmation page.
 
-11. Find the cluster's web address by choosing the ``View`` option form the Kiosk's main menu. (Depending on your chosen cloud provider and the cloud provider's settings, your cluster's address might be either a raw IP address, e.g., "123.456.789.012", or a URL, e.g., "deepcellkiosk.cloudprovider.com".)
+* Find the cluster's web address by choosing the ``View`` option form the Kiosk's main menu. (Depending on your chosen cloud provider and the cloud provider's settings, your cluster's address might be either a raw IP address, e.g., ``123.456.789.012``, or a URL, e.g., ``deepcellkiosk.cloudprovider.com``.)
 
-12. Go to the cluster address in your web browser to find the DeepCell Kiosk frontpage. To run a job (load raw data and download the results) use the ``PREDICT`` tab.
+* Go to the cluster address in your web browser to find the DeepCell Kiosk frontpage. To run a job (load raw data and download the results) use the ``Predict`` tab.
 
-13. The ``Predict`` page on DeepCell.org allows for different job types (ie: nuclear segmentation and or nuclear tracking). Each job type requires a specific model. For example models and data, refer to `DeepCell.org <https://deepcell.org/data>`_.
+* The ``Predict`` page on DeepCell.org allows for different job types (ie: nuclear segmentation and/or nuclear tracking). Each job type requires a specific model. For example models and data, refer to `DeepCell.org <https://deepcell.org/data>`_.
 
 .. note:: The first prediction may take some time as the model server comes online.