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14 changes: 10 additions & 4 deletions docs/usage/pro/frame/tutorials/day-1/first-connection/README.md
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Expand Up @@ -43,6 +43,8 @@ Throughout this process, the FRAME's indicator LEDs will report what it's doing

## Connect to the FRAME's Wi-Fi hotspot

Now that the FRAME has finished booting up, we're ready to connect your computer to the FRAME in order to access the FRAME's software.

The RPi makes a Wi-Fi network from its internal Wi-Fi module; we call this network the FRAME's *Wi-Fi hotspot*.
The name of the Wi-Fi hotspot has the format `openuc2-{machine name}`, where `{machine name}` should be replaced with the RPi's machine name.
For example, if the machine name is `separate-bath-30666`, then the Wi-Fi hotspot will be named `openuc2-separate-bath-30666`.
Expand All @@ -69,9 +71,11 @@ Alternative ways of giving your computer internet access while it's connected to

:::

## Open the FRAME's web browser interface
## Open the FRAME's web browser landing page

Now that your computer has a network connection to the FRAME, we're ready to access the FRAME's software from the web browser on your computer.

Next, open your computer's web browser and try navigating to each of address in the following list, and in the following order, until you find the first one which works for you (which will depend on your computer's operating system and how your web browser is installed):
Open your computer's web browser and try navigating to each of address in the following list, and in the following order, until you find the first one which works for you (which will depend on your computer's operating system and how your web browser is installed):

1. [http://openuc2.local](http://openuc2.local)

Expand Down Expand Up @@ -105,9 +109,11 @@ You can bookmark this page in your web browser for easy access, so that you don'

:::

For now, we will open *ImSwitch*, which is the app for operating the microscopy-related functions of your FRAME machine.
## Open ImSwitch

Now that you have the landing page open in your web browser, we're ready to open *ImSwitch*, which is the app for operating the microscopy-related functions of your FRAME machine.

Click on the "ImSwitch dashboard" link which can be seen under the "Browser applications" section of the screenshot above.
On the landing page, click on the "ImSwitch dashboard" link; it can be seen under the "Browser applications" section of the screenshot above (in the previous section).
The link will open ImSwitch in a new tab, and you will see something like this:

![ImSwitch Live View](./imswitch-live-view.png)
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87 changes: 87 additions & 0 deletions docs/usage/pro/frame/tutorials/day-1/first-sample/README.md
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Expand Up @@ -3,3 +3,90 @@ sidebar_position: 40
---

# First Sample

Now that you've [confirmed that your FRAME was not damaged during shipping](../operational-readiness/README.md), we're ready to view microscopic samples with your FRAME.

In this tutorial, we will preview, save, and view our first images of a microscopy sample.
Along the way, we will see how to adjust imaging settings in ImSwitch's Live View app.

## Open the live viewer

The basic interface for exploring microscopy samples and adjusting imaging settings is ImSwitch's Live View page.
The Live View page is ImSwitch's home page, so it's what we see when we [initially open ImSwitch](../first-connection/README.md#open-imswitch).
We can also open the Live View page from other pages in ImSwitch by clicking on the "Live View" entry in ImSwitch's navigation sidebar.

Once you open the Live View page, it will look something like this:

![ImSwitch app: Live View app](./imswitch-live-view.png)

In the center of the above screenshot, under the "WIDEFIELDCAMERA" tab, we can see a preview camera stream from your FRAME's main camera.
This preview stream has red indicator (which says "LIVE - 16.0 FPS" in the above screenshot) in its upper-right corner which indicates whether the preview is a live preview, as well as the framerate of the preview stream.

## Insert your first sample

TODO: how should the customer safely insert a slide or wellplate into the microscope, without the slide falling into the microscope?

## Explore your first sample

TODO: how should the customer reposition the sample so that the sample will be in the view of the objective lens? How should the customer turn on the appropriate light source to view the sample? How should the customer choose and set good light settings (light source intensity, exposure time, camera gain)?

## Save your first image

To save your first image of your sample, go to the "Capture" panel below the camera stream:

![ImSwitch app: Live View app: Capture panel](./imswitch-live-view-capture.png)

Enter a brief name for the image in the "Description" textbox:

![ImSwitch app: Live View app: Capture panel: Description](./imswitch-live-view-capture-description.png)

Then press the "Snap" button to save the image to the FRAME's internal storage.

## View your first image

To view the image you just saved, press the "Go to Folder" button:

![ImSwitch app: Live View app: Capture panel: Go to Folder button](./imswitch-live-view-capture-go-to-folder.png)

This will display the image file in ImSwitch's File Manager app:

![ImSwitch app: File Manager app](./imswitch-file-manager.png)

Then we can right-click on the image to open a menu with entries to download the image or to preview it in ImSwitch:

![ImSwitch app: File Manager app: context menu: preview with ImJoy](./imswitch-file-manager-imjoy.png)

This will open ImSwitch's ImJoy app.
After several moments, ImJoy will finish loading and open a window with a preview of the image we had saved:

![ImSwitch app: ImJoy app](./imswitch-imjoy.png)

## Download your first image

Now that we've previewed your first image, let's return to the File Manager to download the image to your computer.

Click on the "File Manager" entry in the navbar.
This will return us to the file we had previously selected:

![ImSwitch app: File Manager app: context menu: nav](./imswitch-file-manager-nav.png)

Now right-click on the image again, and click on the context menu's entry to download the image:

![ImSwitch app: File Manager app: context menu: download](./imswitch-file-manager-download.png)

This will open your web browser's dialogue choose a location on your computer for downloading the image.

Then you can view the image (and its associated metadata) in other programs on your computer, such as Napari or Fiji:

![Fiji](./fiji.png)

:::tip

You can configure ImSwitch to save the image directly to a removable USB storage device, instead of saving the image to the FRAME's internal SD card.
When you are acquiring large amounts of data, you should save your data to a removable storage device so that you can transfer it to other computers more easily and more quickly.

To learn how to do this, please refer to our [day-2 tutorial](../../day-2/acquire-data/README.md#to-a-removable-usb-storage-device).

:::

Now that we've acquired, previewed, and downloaded our first image, we're ready to learn how to [set up your FRAME to be able to get remote assistance from openUC2 customer support](../remote-assistance/README.md), [acquire data more efficiently](../../day-2/acquire-data/README.md), [improve your FRAME's imaging settings for your particular sample](../../day-2/imswitch-settings/README.md), and [more](../../day-2/README.md)!
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Expand Up @@ -4,3 +4,62 @@ sidebar_label: Operational Readiness
---

# Check Your FRAME's Operational Readiness

In this tutorial, we will perform some checks to ensure that your FRAME is ready to be operated as a microscope.
Along the way, we will see some basic troubleshooting procedures you can run if your FRAME behaves in way that you don't expect.

## Ensure correct ImSwitch hardware configuration

Because ImSwitch is designed to be used with a variety of hardware configurations (which may involve different detectors, light sources, stages, etc.), ImSwitch needs to be given information about the hardware configuration of your machine.
This is done by selecting one of the preinstalled hardware configuration files in ImSwitch.

If you purchased and received a machine directly from openUC2, then the correct hardware configuration file was already been set for you as part of openUC2's procedures for testing that your machine works.
Here, we will find the name of the correct hardware configuration file for your machine.

First, [open ImSwitch](../first-connection/README.md#open-imswitch).
Click on the settings icon in the upper-right corner of the page in order to open the settings menu, and click on the "ImSwitch Backend Settings" menu item:

![ImSwitch app: settings menu: ImSwitch Backend Settings](./imswitch-settings-menu.png)

This will open a settings page which shows the name of the currently-selected hardware configuration file:

![ImSwitch app: Backend Settings page: current configuration](./imswitch-settings-backend-configuration.png)

In the screenshot above, you can see that the current configuration is called `FRAME2b.json`.

The name of the current hardware configuration file should match what openUC2 customer support communicated to you when the FRAME machine was delivered to you, so you shouldn't need to change anything here.

:::info

If you need to change the hardware configuration file, please refer to our [day-2 tutorial](../../day-2/imswitch-settings/README.md#change-hardware-configuration).

:::

## Perform acceptance test procedure

In order to ensure that the FRAME's hardware wasn't damaged in the process of being shipped to you, we can perform an acceptance test procedure in ImSwitch to check for certain kinds of hardware problems.

To open ImSwitch's Acceptance Testing app, click on the "App Manager" entry in ImSwitch's navigation sidebar:

![ImSwitch app: navigation menu: App Manager](./imswitch-nav-menu-app-manager.png)

On the App Manager page, click on the search box:

![ImSwitch app: App Manager app: search box](./imswitch-app-manager-search.png)

Type "test" to filter the apps, and then click the play button on the Acceptance Test app:

![ImSwitch app: App Manager app: Acceptance Test entry: play button](./imswitch-app-manager-acceptance-test-play.png)

This will open the Acceptance Test app:

![ImSwitch app: Acceptance Test app](./imswitch-acceptance-test.png)

For each action (e.g. "Home X Axis") listed in the app, press the button to perform that action and then answer the question about the result of that action (e.g. "Did the stage successfully home?") by pressing the corresponding button (e.g. "Yes" or "No").

At the end of the test sequence, a test report will be generated summarizing the results of the acceptance test procedure.
If any test failed on a FRAME which you purchased from openUC2, please download the test report and send it to openUC2 customer support at [support@openuc2.com](mailto:support@openuc2.com) so that we can identify and fix any damage to your machine which occurred while it was in the process of being shipped to you.

![ImSwitch app: Acceptance Test app: test report](./imswitch-acceptance-test-report.png)

If all tests passed (like in the screenshot above), then your FRAME is ready for you to use it as a microscope for saving images of your [first sample](../first-sample/README.md)!
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Expand Up @@ -9,7 +9,7 @@ In this tutorial, we will set up remote assistance on your FRAME machine, so tha

## Connect your FRAME to the internet via Wi-Fi

First, let's open the FRAME's landing page in your web browser (we learned how to do this [in the First Connection tutorial](../first-connection/README.md#open-the-frames-web-browser-interface)).
First, let's open the FRAME's landing page in your web browser (we learned how to do this [in the First Connection tutorial](../first-connection/README.md#open-the-frames-web-browser-landing-page)).

Next, open the "Machine administration" link in the landing page's "Browser applications" section.
The Machine Administration app provides a simple way to manage various computer-related settings of the RPi in your FRAME.
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8 changes: 8 additions & 0 deletions docs/usage/pro/frame/tutorials/day-2/acquire-data/README.md
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---
sidebar_label: Acquire Data
---

# Acquire Data

## to a removable USB storage device

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---
sidebar_label: ImSwitch Settings
---

# Adjust ImSwitch Settings

## Optimize camera streaming settings

## Change hardware configuration
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