Getting Started#

Follow the Quick Start Guide below to get started with the Miniscope System right away. It uses Bonsai to connect to a Miniscope v4 via a Miniscope DAQ and validate its functionality. To learn more about the software’s functionality and other software options to acquire from the Miniscope v4, read the Software Guide. For information on using miniscopes for experiments, please refer to the User Guide. You can find more information about the system at large among the Additional Resources.

Quick Start Guide#

../_images/Miniscope_and_DAQ.jpg

Starting with the basics: a system made up of the Miniscope DAQ v3.3 and a Miniscope v4.#

Connecting the Hardware#

Required components: Miniscope v4, Miniscope DAQ, coaxial tether (SMA ↔ U.FL), USB3.0 cable (Micro Type B ↔ Type A)

  1. Connect the Miniscope DAQ to the miniscope using the coaxial tether:

    • Insert the tether’s SMA plug into Miniscope DAQ’s SMA jack labeled Miniscope. Gently hand-tighten the SMA connector until the connector no longer turns:

    photograph of SMA plug going into Miniscope DAQ SMA jack

    • Click the tether’s U.FL connector into the miniscope’s U.FL socket. Take extra care to stabilize the PCB where the connector is attached during connection and disconnection of the tether. Make sure you feel both parts click together to ensure the connector is correctly seated.

    Important

    • Hold the connector PCB firmly from the sides to fix in place so it does not bounce. Otherwise, components can get damaged by scraping PCBs against each other or the body.

    • Avoid inadvertently bending the flex-cables that join the PCBs. Otherwise, the electrical connections inside the flex-cables may break.

    • Align the connector to the socket and press it in without excessive force. If it does not go in easily, realign and try again. Otherwise, the connector can get damaged.

  2. Connect the Miniscope DAQ to a USB 3.0-compatible port on your computer using the high-speed USB cable provided. USB 3.0-compatible ports are usually indicated by a blue color and/or the SuperSpeed mark and are often at the back of PCs.

    Important

    Ensure you establish a reliable USB connection by using a high-speed USB cable and connecting directly to the port instead of through a hub or extension. USB cables longer than 2 meters are not recommended.

    • Insert the cable’s USB3.0 Type A plug into your computer’s USB3.0 Type A jack:

    photograph of usb plug going into computer usb jack

    • Insert the cable’s USB3.0 Micro Type B plug into the Miniscope-DAQ’s USB3.0 Micro Type B jack located on the Miniscope-DAQ’s back face:

    photograph of usb plug going into miniscope-daq jack

    Once all connections have been properly established, you should see all three indicators LEDs on the Miniscope DAQ turn on as in the image above.

  3. Go to Start Menu > Settings > Devices > Bluetooth & other devices and check that the board is listed as Connected to USB3.0, with no additional warnings:

    screenshot of connected devices menu showing the Miniscope DAQ connected to USB3.0

Installation#

  1. The Miniscope DAQ works via USB, so make sure you configure the Operating System’s USB settings to avoid suspension due to power management.

  2. Download and Install Bonsai either as a portable environment or a system-wide application.

  3. Install the following packages from the Bonsai Package Manager , making sure the Package source set to “All”:

    • OpenEphys.Miniscope.Design: An extension of the OpenEphys.Miniscope library that includes graphical user interfaces (GUIs). Installing OpenEphys.Miniscope.Design automatically installs OpenEphys.Miniscope as a dependency.

    • Bonsai.StarterPack: the “standard library” for Bonsai that contains tools that are used in almost every workflow.

Testing the Miniscope’s Functionality#

  1. Copy or download the following workflow using the corresponding icons and paste the contents or open the .bonsai file in Bonsai:

    uclaminiscopev4-miniscopedaq-quick.bonsai
    uclaminiscopev4-miniscopedaq-quick

    • The UCLAMiniscopeV4 node represents a UCLAMiniscopeV4 source operator as indicated by its node’s green color and the orientation of its grey arc. Source operators produce data.

    • The UCLAMiniscopeV4 operator’s output (Bonsai.Miniscope.V4Frame) has four members. They can be accessed by right-clicking the UCLAMiniscopeV4 node and hovering the cursor over the Output option in the pop-up menu. Left-clicking on one of these members automatically places a new MemberSelector nodes. These nodes can also be placed by searching modules in the search bar in the Toolbox pane or the using the Ctrl+E hotkey.

    • The MemberSelector operators are transform operators as indicated by the nodes’ blue color and lack of grey bar. Transform operators transform data. The MemberSelector operator transforms data by selecting one or multiple members of its input to output.

    • In this workflow, the Image and Quaternion members are selected from Bonsai.Miniscope.V4Frame to be visualized.

  2. Using the drop-down list, set the UCLAMiniscopeV4 operator’s Index property to the value that corresponds to the index of your miniscope.

    screenshot of UCLAMiniscopeV4 node properties for index

    Note

    If there is no value populated in the drop-down, check the hardware connections. If there are multiple Miniscope DAQs connected to your PC, iterate through the index values while testing the node’s functionality to verify what index corresponds to each miniscope.

  3. Start the Bonsai workflow by left-clicking the green Start button at the top of the Bonsai workflow editor or by pressing F5. Once the workflow is running, you can test various features:

    Real-time Data Visualization

    Image Data:

    Double left-click the Image node. This displays a real-time visualization of image data from the sensor. Try imaging a sample such as a tissue paper. Confirm that the magnified image of the sample appears in the Image node visualizer.

    animation of demonstrating miniscope data
Orientation Data:

Double left-click the Quaternion node. This displays a real-time visualization of quaternion data which represents the miniscope’s orientation. Right-click the visualization, and left-click the drop-down menu. Set the value in the History Length field to 100. Reorient the UCLA Miniscope v4. Confirm the quaternion visualization responds accordingly. To learn more about how to interpret quaternion data, visit the IMU Data article in the Open Ephys Wiki.

animation of demonstrating quaternion data

Miniscope Settings Configuration

Left-click the UCLAMiniscopeV4 node to access the Properties pane on the right.

Frame Rate:

Change the FramesPerSecond value by left-clicking the corresponding field’s drop-down menu located in the Properties pane and selecting a different option. Frame rate and exposure-duration-per-frame are inversely related, so higher frame rates produce darker images. Use this information and look at the Image node visualizer to confirm that the frame rate adjusts according to the FramesPerSecond value. A discerning eye can also notice changes in frame rate, but that requires a moving image.

animation of changing miniscope fps
Sensor Gain:

Change the SensorGain value by left-clicking the corresponding field’s drop-down menu located in the Properties pane and selecting a different option. Look at the Image node visualizer to confirm that the sensor’s gain is adjusted according to the value of SensorGain value.

animation of changing miniscope gain
Excitation Light Intensity:

Change the LEDBrightness value by left-clicking the corresponding field’s drop-down menu located in the Properties pane and sliding the scrollbar. Confirm that the intensity of the excitation light adjusts according to the LEDBrightness value.

animation of changing miniscope excitation light intensity
Dynamic Focusing:

Place the miniscope approximately its working distance away from the sample. Change the EWL value by left-clicking the corresponding field’s drop-down menu located in the Properties pane and selecting a different option. Look at the Image node visualizer shifting in and out of focus according to the EWL value.

animation of changing miniscope focus

Find out how to record image and orientation data, how to perform automatic commutation to avoid the tether from twisting, how to gate data acquisition with a hardware trigger, and more in the Software Guide.

Powering off the system#

The Miniscope DAQ does not have an on/off button. When you are done with acquisition, close the software and unplug the board from USB and/or power.