Getting Started

Welcome to ARTiMiS! Your instrument arrives fully assembled and ready to use after a little bit of setup. This guide takes you from unboxing to a fully set-up instrument ready to run your first sample.

What’s in the box

ARTiMiS instrument
ARTiMiS sample tube attachment
Power supply + outlet adapter
Small form factor peripherals: display, keyboard + mouse (international shipments: shipped separately)
Replacement consumables: tubing, microfluidic chip, sample tubes
Access tools: hex wrenches for M2 and M3 screws
Spare components: replacement gasket washers, product feet, and fasteners

Unpacking the device

Remove the device from its foam packaging, taking care to store the included documents somewhere safe. It is also recommended to retain the original box and packing materials if an RMA of the instrument is necessary at any point in the future.
Remove the two pieces of orange tape from the lid of the device, retaining the cap to the leveling screw compartment.
Remove the two black thumbscrews from the top and front of the access door.
Locate and remove the two pieces of orange tape used to restrain the tubing in transit.
Locate the removable “microfluidic chip sled” in the middle of the device.
Open the right side door, exposing the optical compartment and stage hand controls.
Loosen the right-side stage tightening thumbscrew so that the microfluidic chip sled from (5) can be freely moved forward/backward.
After pulling the chip sled to a more comfortable position, remove the last piece of orange tape affixing the chip holder to the sled base.
Attach the sample tube attachment to the front of the device via its magnetic snapping mechanism.

Set the instrument on a stable, level surface with sufficient room to co-locate peripherals and power supply brick.

Your ARTiMiS unit is now ready to be powered on.

Powering on the device

Connect the power supply to the instrument and to a wall outlet. Attach the 4-pin DIN connector from the power supply to the instrument, and attach the outlet socket adapter to the wall outlet.
If using the included display peripheral: Unpack the display and connect to the instrument via HDMI, accessible on the back of the instrument. (Note: after initial setup and network connection, the instrument can be controlled via another device on the same network, if you prefer to operate the instrument in “headless” mode.)

Important: Connect your display to the instruments HDMI port BEFORE powering on the instrument for the most reliable display connection.
If using the included keyboard + mouse peripheral: Unpack the keyboard + mouse.
- If using a Logitech MK250 shipped in the same box as your instrument, your peripherals connect via Bluetooth and should be pre-paired. WAIT to turn on your peripherals until AFTER you have booted your instrument.
- If using a different model, it may include a USB dongle adapter. Insert this into one of your device’s available USB ports.
- If using a Bluetooth-only peripheral that did not ship in the same box as your instrument, you may require the use of a separate USB-capable mouse to open the Bluetooth Connections menu on your instrument’s desktop for initial pairing. You may then freely use the Bluetooth-only peripherals and return your borrowed mouse to its proper home.
Press the power button at the back of the instrument. The illuminated latching power button should stay pressed and its LED will light up if properly connected to power. The instrument may take up to a minute to start up. Your instrument should boot to a desktop environment, visible on your connected display.
If using a Bluetooth-only keyboard + mouse peripheral, turn on these devices after the instrument is fully powered on and idling on the desktop for the most reliable connection experience.

ARTiMiS runs on the Raspbian Operating System, a Linux OS. Please take a moment to familiarize yourself with the desktop layout if this is your first time using this operating system:

The desktop is arranged similar to other desktop environments you may be familiar with on Windows or Mac, featuring apps, folders, etc. that are made visible on the desktop.
The default taskbar location on your instrument is at the bottom of the screen, and functions similar to taskbars you may be familiar with on Windows or Mac.

On the left side of the taskbar:

Icon	What it does
Raspberry Pi	Equivalent to the Windows or Apple icon. Clicking it opens a menu to access installed applications and other programs.
Globe	Launches a Chromium web browser.
Folder	Launches the file explorer.
Terminal	Launches a command line terminal.

On the right side of the taskbar:

Raspberry Pi Connect
Bluetooth Devices
WiFi Connections
CPU Temperature Monitor
Date/Time/Calendar

Connecting to the Internet (Recommended)

Click the “WiFi Connections” icon on the taskbar, third from right in the right-side icon group. The icon will either display as a “fan”-shaped Wi-Fi type icon, or two vertical lines with red “x” icons, depending on network status.
Browse available networks to find your desired wireless network.
Enter your credentials, then wait to connect to the internet. The icon should show a fan-wave design, with colored arcs indicating network connection strength.
- Red “X” markings on the icon indicate a failed network connection.
Test your connection to the internet by either opening the Chromium web browser, or running a Terminal CLI command such as ping -c 3 google.com
- (Optional) Set a password for the built-in Chromium keychain, or close the popup to defer setting.

Alternatively, use the Ethernet port at the back of the instrument to connect directly to a wired network.

While not required, connection to the internet will allow your instrument to automatically detect and pull software updates. Updates include bugfixes, security patches, and new features to improve your instrument.

Launch the control app

The recommended way to run ARTiMiS is directly on the instrument, using the included display and keyboard + mouse:

On the desktop, double-click the ARTiMiS icon (the Skopii logo).
A small launcher window will open. If your instrument is connected to the internet, it checks for software updates:
- If an update is available, you can choose Update to install it (recommended) or continue on your current version. The launcher can also roll back to a previous version if you ever need to.
- If you’re already up to date, the launcher continues automatically after a few seconds — no action needed.
The control app then opens full-screen in a captive browser.

Tip: The launcher checking for updates needs the internet, but the control app itself runs entirely on the instrument — no internet connection is required to run samples.

Opening the app from another device (optional)

While the app is running, you can also open it from a computer, tablet, or phone for convenience — for example, to review results from your desk:

Make sure your device is on the same network as the instrument.
Open a web browser (Chrome and Edge work best) and go to the web address printed on your quick-start sheet. It looks like:
```
http://artimis-00042.local:8000
```
where 00042 is the five-digit middle portion of your instrument’s serial number — for example, serial AM1-00042-7 becomes artimis-00042. Don’t forget the :8000 at the end.

You can find your serial number on the sticker on the instrument’s back panel, between the USB/HDMI ports and the power connector.

You can open the app on more than one device, but only one person should run a sample at a time.

If the address doesn’t load:

Double-check that both devices are on the same network.
Make sure the control app is running on the instrument (launch it from the desktop as described above).
Try the instrument’s network (IP) address instead of the .local name if your quick-start sheet lists one.
See Troubleshooting for more help.

Initial sign in

The first time you load the ARTiMiS app, you will be prompted to create an organization administrator account. This account will serve as the local admin with the ability to reset and manage additional user accounts on this device.

Select a display name - your name, ADMIN, etc.
Select a username for logging in with in the future.
Enter a secure and memorable pass-word or pass-phrase.

After confirming your credentials, you will be shown a short recovery phrase. Write this phrase down and keep it safe, as it will be the only way to recover a local account in the event that you forget your password.

Note that all accounts, including the administrator user, can be forcibly reset should you ever become hard-locked out of your accounts, but this may cause loss of saved settings presets and profile customization. Raw sample data will be unaffected, but metadata such as operator ownership may become orphaned.

Creating additional operator accounts

After you’ve created a local administrator account, you can sign out to create new operator accounts. Operator accounts can manage their own settings profiles, samples, etc., but do not have authority to reset or recover other local accounts.

When the instrument asks you to sign in, you have two options:

PhycoSight Cloud account — sign in with the same email and password you use at phycosight.com. This links your runs to your organization and lets you upload samples to the cloud. If you don’t have an account yet, you can create one at phycosight.com.
Device account — a local account that works entirely offline, with no cloud or network required.

Fluid integrity test

To test a sealed fluidic line through the instrument, perform the following setup test:

Prepare 1-2mL of clean water in a 1.5mL or 2.0mL sample tube, and place it in the sample tube front attachment (any position).
Pull ARTiMiS intake (right) and discharge (left) micro tubing through the guide grooves at the front of the device.
Place the two ends of the tubing in the sample tube.
In the Operator UI of the ARTiMiS App, locate the “Fluidics” section of the “Controls” tab, then the “Circulate” button.
Press the “Circulate” button to manually toggle on/off the fluidic system.
Observe the water sample being pulled through the intake tubing line, into the microfluidic chip, and through the discharge tubing line.
(Optional) Select the “Fine Control” submenu to increase the power level of the pump to between 40% and 70% to expedite the test.
After confirming the test volume completes a fluid circuit, remove the intake tubing from the test sample tube. Keep the discharge tubing submerged to avoid spilling your sample.
Continue circulating to observe the air volume displacing water through the full tubing line.

Once all liquid has dispensed from the tubing line, the test is complete.

Alternatively, you can use a full “source” sample tube and an empty “sink” tube to run the test hands-free, at the cost of consuming an extra sample tube. Place the intake tubing line into the source and the discharge into the sink, then begin the test.

Aligning the flow channel

When using ARTiMiS for the first time, the flow channel will not be aligned to the optical assembly. The microfluidic chip contains 16 parallel flow channels. ARTiMiS units ship with tubing configured for the #2 channel (#1 and #16 are occluded by the sled). Examine the spare microfluidic chip included in your consumables kit for a closer look.

In the Operator tab of the ARTiMiS App, locate the large preview pane in the center of the screen, and preview control bar below it.
Toggle the live preview feed on.
With the stage thumbscrew loosened to allow the sled to move freely forward/backward, pull the sled to the front of the device until the #2 channel is roughly aligned with the guide marks on the left/right sides of the stage. The guide marks look like inward-facing triangles to indicate approximate optical alignment. You can open both side doors to shed more light on the situation.

To find the channel, slowly push/pull the sled, noting a series of horizontal “bars” passing by in the camera preview viewport. These are the side walls of the flow channels in the chip. There are several ways to locate and lock into the active channel.

First, use the manual focus adjustment to set the current focus position to ~5-7. Your instrument was pre-calibrated for these focus positions to be within or very near to the depth of the channel. Note that for strategies 2 or 3 below, it may be helpful to scan through focus positions 1-11 using manual control to help assist in locating objects if your instrument’s z-axis is slightly out of alignment.

Geometric Alignment: The #2 channel is the first visible channel from the “bottom” of the chip, from the camera’s perspective. Pull the sled out until the camera’s view is black (obscured) in bright field. Push the sled so that the FOV is bright again, then locate the first pair of horizontal bars. These should correspond to the #2 channel.
Residual Bubbles: If you completed the fluid integrity test, there will likely be a small number of bubbles visible in the #2 microfluidic channel. Scan the “bottom” of the chip from the camera’s perspective for an array of small circular shapes (bubbles), or hemispheric shapes attached to one or both of the horizontal bars. These bubbles will only be present in the recently-wetted #2 channel. Note that brand new chips are particularly hydrophobic, so there is a chance there are few to no bubbles visible in the field of view.
Live Confirmation: If geometric alignment or residual bubbles fail to provide strong indications of having identified the #2 channel, load a live sample containing suspended particles following the same procedure as steps 1-6 of the fluid integrity test. As before, scan the chip looking for a flow path containing suspended particles.

Common Gotchas:

The microfluidic chips inherently have small pieces of dust, debris, and surface marks on their upper and lower faces. These can appear to be “the sample” at first glance. How to rule out: if similar particles remain in focus when pushing/pulling the sled past multiple flow channels without adjusting the focus position, you are more than likely focused on the top or bottom of the microfluidic chip and not “in” the flow channel.
In an array of seemingly identical “bars” or “lines” of the same orientation, it is possible to be looking in between flow channels instead of within them. How to rule out: the channels themselves are roughly 40% as wide as the between-channel gaps. Regions where the channel edges are close together, just out of frame on the top/bottom of the viewport, correspond to being “in” a channel. If small movements pushing/pulling the sled bring the top/bottom bar into the field of view, you are likely in a channel. This perception will improve with experience.

Locking the configuration

After aligning the flow channel to the optical path, the instrument is ready to be locked down and put into service.

Tighten the loosened thumb-screw to secure the sled in place. A gentle tug on the sled should not move it when fully tightened. Recommendation: Tighten the stage clamp just enough to securely hold the sled without over-tightening, which can reduce the lifespan of the component.
Make final touches on alignment while tightening the sled clamp: having a channel edge in-frame can lead to erroneous detections and inaccurate particle concentration estimates. The final view should be entirely “in” the channel, with neither edge visible in the preview window.
In the “Operate” tab, navigate to the “Fluidics” section and the “Fine Control” sub-menu. Toggle the “Valve” on, to open the valves. A click should be audible when doing so.
Physically place the tubing into the left and right valves in the middle of the open compartment. Either pull the tubing slightly so that it radially contracts under tension, and slide it into the valve opening, or use a small blunt instrument to “stuff” the tubing into the valve opening. Toggling the valve button should open/close the plunger, compressing and releasing the gripped tubing.
It is recommended to have minimal slack on the chip side of the valve. Tubing should rest comfortably on the small riser between the microfluidic chip and the valve, without drooping or sagging.
Once the stage has been locked with its thumbscrew, and tubing is fully inserted into the valves, ensure that the tubing exits the instrument by the front cutouts.
After confirming, all side doors and the main access door can be closed. Optionally use the thumbscrews to secure the main access door, or allow the magnets to hold it in place.
Note that in new instruments, it may be necessary to press the main access door into the housing once seated, as the sealing gasket partially resists the pull of the magnets when the door is gently re-attached.

Your instrument is now ready to process your first sample.

Shutting down the device

It is especially important if performing disk-write operations like running samples, collecting data, or changing configuration settings, to properly shut down both the application and the computer inside ARTiMiS before cutting power to the device. Loss of power during critical write operations can corrupt data files, including sample data, settings, and potentially the operating system itself.

When finished with a session on the device, close the ARTiMiS App, for example via the “x” button on the title bar.
Navigate to the “Raspberry Pi” button on the taskbar in the lower left corner of the screen (equivalent to “Apple” or “Windows” icon).
Select the Shutdown option.
Select the Shutdown option from the popup menu.
Wait for your display to show a “no signal” message confirming that the computer has successfully fully powered down.
Press the physical power button on the back of your instrument to cut power to the device.
Note that when plugged in and powered on, the instrument’s case fan will continue to run even if the ARTiMiS computer is turned off. This is both a thermal safety feature and an audible reminder that the device is still powered on even when shut down.

Where to next

First Sample Run — a guided walkthrough of the control app and your first measurement.
External Storage — using a USB drive and where your samples are saved.
Troubleshooting — fixes for common issues.