Tutorial

Press [H] at any time to open the help and settings menu.

Plan an insertion in six minutes

If you want the quick introduction to Pinpoint, this video will get you all the critical information for planning your first recording. The rest of the tutorial sections go deeper into each topic and explain some of the hidden settings that you can tweak to make Pinpoint work for your specific use case.

Overview

Pinpoint presents you with an interactive 3D scene where you can plan and test different probe insertion trajectories. The scene view shows the mouse brain ( 1) composed of 3D models built from the Allen Common Coordinate Framework annotations and (2) the probe 3D model, showing in white the active recording region. The scene view and probe can be rotated and moved by clicking and dragging with your mouse, see the section titled Controls, below. (3) The rotation gizmo helps you understand the orientation of the brain, with Yellow representing the Dorsal-Ventral axis, Red the Anterior-Posterior axis, and blue the Left-Right (or Medial-Lateral) axis. Double-clicking the gizmo will snap the camera view to the corresponding planar view (i.e. Axial, Coronal, and Sagittal).

Pinpoint interpolates the recording region on the probe in two viewports to help you understand where your electrodes are placed in the brain. The probe UI ( 4) shows you a linear interpolation through the recording region. The in-plane slice (5) shows you a view of not only the probe but also the surrounding regions. You can click regions in the in-plane slice to highlight them in the 3D scene. You can also highlight regions of interest by searching for them in the search panel (6). Click a region turns it on and off and pressing the * Clear* button removes all highlighted regions. The snap-to-area button ( downward arrrow) moves the probe tip to the center of that region.

To set up a new probe, select the corresponding button the new probe panel ( 7). By default, probes are spawned at Bregma. You can change the reference coordinate in the Atlas settings. When you have multiple probes in the scene you can click on the probe objects to switch the active probe, or you can click on the probe panels on the left side of the screen.

The coordinates of a probe are shown in the last panel (8) and can be copied to the clipboard using the download icon at the top right. When the probe is outside of the brain we display the tip coordinate and angles. When the probe is inside the brain Pinpoint computes for you the brain surface coordinate and * depth* of the probe, which are the coordinates you would need to re-create an insertion. See the surgery section for a few important details.

Quick settings

The quick settings panel provides easy access to the information about the active probe in the scene. Using the panel you can tweak the entry coordinate by changing the AP/ML/DV position data or change the insertion depth. You can also adjust the insertion angles.

The three buttons on the top right lock the probe (preventing accidental keyboard or mouse movements), duplicate the probe in the scene, and download the probe data to the clipboard. You can paste the copied data into any text editor.

The bottom row has the Accounts dropdown where you can choose which experiments this probe is saved in, as well as the snap to dura button and home button.

The home button moves the probe back to the current reference coordinate (defined in the Atlas settings). The snap to dura button snaps the probe back to the surface of the brain, moving only along the depth axis.

Camera controls

Probe controls

Click + Drag

To control your probe with mouse clicks and dragging:

1. Left-click and hold on the probe object

2. Press and release any of the axis keys on your keyboard, the axis should become visible in the 3D scene

3. Continue holding the mouse and drag the probe along that axis.

The axis keys are [W/S] for AP, [A/D] for ML, [Q/E] for DV, and [Z/X] for depth. Note that in some views it may be hard to drag along a particular axis (e.g. in the default axial view you can’t drag a probe along the DV axis, because the axis is not visible).

Keyboard

You can also press the keyboard keys to move the probe along that axis in 10um units. Hold SHIFT to move in 100um units. Hold CTRL to move in 1um units. Pressing and holding a key moves continuously.

Use [W/A/S/D] to move the probe along the AP or ML axis. Use [Z/X] to move the probe along the DV axis.

USe [Q/E] to rotate the probe azimuth, which corresponds to the angle of the probe manipulator relative to the brain.

Use [R/F] to change the angle of the probe on the manipulator (restricted to 0-90 deg range).

Use [1/3] to spin the probe along the axis of the probe shank. Note that NP2.4 probes spin around the leftmost probe shank when looking from the back.

Probes can be deleted with [Backspace]. To recover a probe you didn’t mean to delete press [CTRL + Backspace].

Recording region

Once the probe is at the position and angles you want, you can adjust the recording region size (in the settings) and position (using [T/G]) to match what you plan to do in your recording and adjust the insertion depth accordingly.

Designing a trajectory and probe coordinates

Probe coordinates

A probe insertion is defined by a target coordinate in the brain and a set of angles to reach that point. When you export a planned insertion Pinpoint will compute the brain surface coordinate and depth of the probe, which you will need to actually perform your experiment.

Note that insertions are defined in a Coordinate Space with a particular ** Transform**. The space defines the rotation of the axes relative to the reference point (i.e. which way do AP/ML/DV go relative to Bregma). By default all insertions in Pinpoint are defined in the common coordinate framework space, using the IBL axis conventions, these can be changed in the settings. The standard transform is the Toronto MRI transform, which was based on the average of 12 adult C57 mice. You can read more about the transform options on the in vivo alignment page.

Help and settings

The help and settings menu is accessed by pressing H. Press H again to close the window. The tabs (1) on the left side switch between the different sub-menus.

Rig components

Areas & Atlas options

Ephys Link

Pinpoint can be connected to Sensapex manipulators enabling experimenters to automate the placement of manipulators as well as observe live where probes are placed inside the mouse brain.

These features are only available on the Windows Desktop build of Pinpoint they will not run in the web browser.

To enable this feature, an instance of an Ephys Link server must be running on the local network. Please see the instructions here on how to install and run a server.

Connecting to a server

1. Press [H] to open the settings menu

2. Switch to the “Ephys Link” tab

3. Fill in the server’s IP address

4. And the port number

5. Click “Connect”. Upon success, the connect button will read “Disconnect”

6. Manipulators by default spawn as “left-handed”. Use the drop-down menu to change the handedness of each detected manipulator.

   1. Handedness determines the orientation of the manipulator and which direction it moves. Handedness is determined by which side of the manipulator the probe will be mounted on.

7. Press [H] again to close the settings menu

Linking a probe in the planner to a manipulator in real life

1. Spawn the corresponding probe (NP 1.0/2.0/2.4) in the planner scene

2. Press [H] to open the settings menu

3. Switch to the “Ephys Link” tab

4. Using the dropdown for each probe, select the desired manipulator to connect to. Only manipulators that are connected to the server will be listed.

5. Upon connection, the probe’s stereotaxic position will be used as the zero coordinate all movements will be relative to. This zero position can be edited manually through the text boxes or by clicking the home button to reset the position to the current probe position.

6. The probe’s offset from the brain surface and which direction it is calculated can be adjusted here. The offset is the distance from the probe tip to the brain surface. This offset can be determined as the distance from the tip to the brain surface along the DV axis or the probe’s depth axis.

Quick settings

The quick settings panel

Account

The Accounts tab in the settings allows you to save insertions across computers. Insertions are stored in experiments. One insertion can be shared across multiple experiments.

1. Register a new account, we kindly ask that you use an email address so that we can keep in touch about major updates to Pinpoint in the future. We won’t give away your email or send a message more than once or twice a year.

2. Log in to your account by providing the username and password. Leave the “stay logged in” toggle checked if you are on a private computer.

3. Open the experiment edit panel to add and remove experiments and re-name them. Experiments are just buckets, you can use them in any way you want: to represent mice, to actually represent different experiments, to represent differents sets of insertions targeting particular brain regions, etc.

4. Select the current active experiment from the dropdown. This will change the visible list of insertions below.

5. The insertion list shows the insertions in the active experiment. You can rename insertions, delete them from the experiment, and enable/disable them in the 3D scene. Coming soon: we will add options to mark insertions as “recorded” so that we can calculate coverage maps for experiments.

6. Any time your local data is out-of-sync with the data stored on the server the “unsaved changes” message will appear. If you are using Pinpoint in a browser please note that unsaved changes do not get saved if you exit the browser, the program auto-saves changes about once a minute. If you are using Pinpoint in a desktop app, exiting will automatically save all changes.

Surgery

To use your coordinates for a surgery, rotate the manipulator to match the azimuth angle (phi) and set the probe elevation angle (theta). Then move your probe tip to Bregma and zero your manipulator.

Translate your probe using the manipulator to match the AP/ML/DV brain surface coordinate provided by Pinpoint. If your probe is rotated off-axis use the * convert AP/ML to probe axis* setting so that you can match the Forward/Side/DV position instead. Use caution! You may reach the brain surface before you reach the DV value specified by Pinpoint, don’t break your probe!

Once the probe is touching the dura, zero the depth axis and insert until you reach the specified depth.