Pinpoint: trajectory planning for multi-probe electrophysiology and injections in an interactive web-based 3D environment

Reviewer #1 (Public Review):

Summary:
Previously, researchers targeting certain brain areas in mice have relied on manual reconstruction of 3D trajectories based on published atlases of 2D sections in standardized anatomical planes. Over a decade ago, Leica's AngleTwo software provided an early proprietary software interface to rodent atlases based on 2D graphics. However, the more recent advent of open-source 3D gaming engines and CAD software (here the authors used Unity) and the adoption of a common 3D atlas framework (the Common Coordinate Framework, or CCF, from the Allen Institute) by the neuroscience community have enabled more advanced targeting based on 3D anatomy, as primate researchers and human clinicians have done previously with MRI data using bespoke and commercial software solutions. The Neuropixels Trajectory Explorer (https://github.com/petersaj/neuropixels_trajectory_explorer, by Andy Peters) pioneered a software interface to the 3D mouse atlas for electrode insertions, and here Birman et al. have built on the aforementioned previous efforts to provide the most comprehensive trajectory planning software in mice to date, which they call Pinpoint. The most critical improvement lies in the ability to model the experimental rig and instruments in the same 3D environment as the atlas, since previously researchers needed to iteratively guess and check whether instruments physically fit with each other and the other constraints imposed by the rig. Other key features include coordinate transforms to map the CCF to more accurate in vivo anatomical data, as well as an API and hardware interface to commonly used micromanipulators.

Strengths:
The feature set in Pinpoint makes it the best available software for planning instrument trajectories given geometrical constraints. Additionally, the documentation and open-source nature of the software should allow many extensions and improvements in the future, and as the authors note, it can also be used as a powerful teaching tool. Especially as researchers continue to push the boundaries of concurrent electrodes and optical fibers or other instruments within a single brain, this software will be of great use for neuroscience.

Weaknesses:
Although Pinpoint enables instrument insertion planning with geometrical constraints for the first time and has many other novel features, it remains to be quantified how useful it is in terms of time/efficiency gains and accuracy of planned trajectories. For instance, although using a coordinate transform to MRI anatomical data is more accurate than the CCF alone in principle, users will need to verify how much this improved planning ability translates to time saved and/or improved trajectories as reconstructed from histology of dyed electrode tracks. The utility of the hardware interface for automating experiments versus the risk of damaging instruments with such an approach also remains to be quantified. Researchers using experimental subjects other than adult mice will have to wait for future integration of their atlases of choice, although the open-source nature of the project invites others to try adding this and other desired features themselves.

Reviewer #2 (Public Review):

Pinpoint by Birman et al. serves not only as a probe trajectory planning tool but also offers a far richer suite of functionalities. It provides a simple and intuitive environment that users can learn within minutes and start planning trajectories for multiple probes based on the Allen mouse brain atlas. Pinpoint further includes two MRI-based transformations to better map the Allen atlas to live brains. It features a coefficient to adjust for different Bregma-Lambda distances and includes a mouse skull model to provide a better approximation of the craniotomy coordinates, rather than the coordinate of the point of insertion on the brain. It also offers tools to link the application to manipulator controllers to visualise the position of probes in the brain in real-time. Remarkably, most of these features are available right from the web browser, without the need to install anything or any coding knowledge.

The authors developed an open-source and well-documented software. Although I did not test it myself, it can communicate with the most common recording softwares (Open Ephys, SpikeGLX) and manipulators (New Scale, Sensapex) in the field. The current level of support by the developers on GitHub is reassuring, and I hope this continues as Pinpoint matures into a more stable and robust version.

Reviewer #3 (Public Review):

Summary:
Birman and colleagues have introduced an invaluable tool designed specifically for electrophysiologists, simplifying the precise planning of trajectories for placing high-density probes within designated locations. Pinpoint offers users an interactive 3D environment within which they can explore electrophysiological trajectories within the anatomical context of the mouse brain. Within this environment, users can visualize the probe, target regions, and the constraints imposed by their experimental setup. Advanced users also have the flexibility to customize the entire Pinpoint scene to align with alternative coordinate systems and rig geometries. In cases involving multiple-probe recordings, Pinpoint shows 3D paths while issuing warnings about potential collisions. Additionally, Pinpoint can account for the individual variability in brain size among mice.

Strengths:
Pinpoint provides real-time visualization of current brain region targets alongside neural data. Anatomical targeting information is accessible live during recordings. This is made possible through two sets of features: hardware that allows Pinpoint to communicate with micro-manipulators and software that broadcasts the current location of each recording channel to data acquisition software. Researchers can monitor the precise positioning of their probe during insertion and observe the anatomical locations of live electrophysiology data throughout an experiment, enabling them to make corrections if necessary.

Weaknesses:
1. Pinpoint's novelty lies in its ability to be linked to data acquisition programs and electronic micro-manipulators. However, a similar program, Neuropixels Trajectory Explorer, was released before Pinpoint with comparable features. Please refer to https://github.com/petersaj/neuropixels_trajectory_explorer. It would be beneficial to clarify the distinctions between these two applications and discuss on the necessity and advantages of creating Pinpoint.

2. Currently, in Pinpoint, users can only select one area of the mouse brain for probe placement and then use the controller to adjust the probe´s position if they wish to target multiple brain areas. This can complicate planning when inserting multiple probes. It would be advantageous to have the option to choose the specific areas the probes are to traverse, with Pinpoint automatically suggesting the most optimal trajectories while avoiding potential collisions. While this may require additional development, a comment on this possibility would be appreciated.