Neuropixels Trajectory Explorer / MPM System Pathfinder Software update

NEW SCALE NEWS

LIFE SCIENCE LAB AUTOMATION EDITION

March 2023

Dear Colleague,

I have been having a lot of fun with the Neuropixels Trajectory Explorer (NTE) software from Andy Peters (Peters Lab, Oxford), as we work to link this amazing open-source tool to into our MPM System Pathfinder software.

Andy recently provided instructions showing how to plan an example trajectory from V1 to LGN. The document (on Andy's GitHub wiki page) shows how to highlight V1 and LGN in the Allen Institute CCF atlas, then move the probe in NTE until it touches both regions - working alternately through the Coronal, Sagittal and Horizontal views in the atlas. You then can see the atlas and the stereotactic coordinates of the start and end point of the probe, as well as what we call the Polar Angle and Pitch Angle of the MPM System (Azimuth and Elevation in Andy’s menu).

When you enter the start and stop coordinates from NTE into the MPM System’s Pathfinder software, Pathfinder calculates the Arm Height and Arm Length to hit those targets at that Polar Angle and Pitch Angle. Then you just:

set up the MPM System according to those parameters
touch Bregma and Lambda to set up stereotactic mode
click a button to move the probe to the start point
hit “Insert” at the slow speed that you choose.

In a multiprobe environment, you can move each probe to its start point and then insert them all simultaneously.

As you perform the insertion, you can see the probe moving through the atlas in NTE. The side bar shows the probe tip location as it progresses through the brain. Here’s how it looks at the end of the insertion:

SCREEN SHOTS showing Trajectory Explorer and MPM Pathfinder after probe insertion

NTE is really an amazing tool and will provide fabulous productivity and accuracy benefits to MPM System users. Our Pathfinder software with integration to NTE is currently in beta testing.

Contact me if you would like an interactive, online demo of Pathfinder (beta) and NTE.

- Ed Friedrich

FROM THE RESEARCH LABS

Allen Institute shares protocol for inserting multiple probes in awake, head-fixed mice

Allen Brain Observatory Neuropixels recording rig, from the paper in Nature Protocols.

As the creator and supplier of the Multi-Probe Manipulator System (MPM), we often are asked to recommend support equipment and procedures to optimize the process of inserting multiple silicon probes in awake, head-fixed mice.

A team at the Allen Institute recently published in Nature Protocols the step-by-step process they use to insert six probes into the visual cortex of a mouse.

We developed the MPM system and software in collaboration with this Allen Institute team, particularly under the mentorship of Josh Siegle. Since they have successfully performed experiments with hundreds of mice, we think their protocol paper likely contains the answers to many of the questions we receive.

FROM THE RESEARCH LABS

MPM System supports research into cellular-level mechanisms underlying brain function

Researchers at Stanford University use the MPM Multi-Probe Micromanipulator for in-vivo electrophysiology with optogenetic stimulation. They published results in an article, Cell-type-specific population dynamics of diverse reward computations, in the 15 September 2022 issue of Cell.

The researchers used Neuropixels 2.0 probes, positioned using the New Scale Technologies MPM Multi-Probe Manipulator System and controlled by the Janelia Research Campus SpikeGLX software, for the acute in-vivo extracellular electrophysiological recordings, with optogenetic perturbation, acquired at 30 kHz.

Read more about this work

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New Scale Technologies develops and manufactures the smallest and most precise closed-loop positioning solutions available. Our “all-in-one” M3 Smart Modules with built-in controllers are easy to integrate with handheld and portable instruments. We enable smaller, smarter imaging systems, scientific instruments, medical devices, aerospace and defense systems and more. Our customers achieve the fastest results with the lowest total cost.

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