A multimodal imaging-guided software for access to primate brains

Abstract

Background: Imaging-guided access to the brain has become a routine procedure for various research and clinical applications, including drug administration, neurophysiological recording, and sampling tissue. Therefore, open-source software is required to handle such datasets in these specific applications.

New methods: Here, we proposed an open-source tool utilizing different imaging modalities for automating the steps to access the brain. This tool provides means for easily calculating the coordination of the area of interest concerning a specific point of entry. The source and documentation are available at this link.

Results: We have used this software for three different applications: electrophysiological recording, drug infusion in the nonhuman primate brain, and guided biopsy procedure in the human brain. We performed a neural recording of two monkeys' prefrontal cortex and inferior temporal cortex using this software in submillimeter resolution. We also applied our procedure for infusion in the putamen and caudate nuclei in both hemispheres of another group of rhesus monkeys with histological proof in one animal. More so, we validated this software in the human subjects that underwent biopsy surgery with the commercial software used in human biopsy surgery.

Comparison with existing methods: Our software uses different imaging modalities by co-registering them. This will provide structural details of the skull and brain tissue. We can calculate each brain region's coordination at the point of entry by re-slicing the images. Atlas-based image segmentation were implemented in our software. Three mentioned applications of our software in neuroscience will be further discussed in this paper.

Conclusion: In our procedure, working with different imaging modalities provides a precise estimation of the specific region in the brain related to the location of implants or stereotaxic frames. There is no limitation to using metal implants in this procedure.

Keywords: Co-registration; Electrophysiology; Image-guided software; Re-slicing.

Fig. 1

The diagram of pyRECaid software. The software involves three main functional forms. The image data including MRI or CT were imported in both main and co-registration forms. In co-registration, images series were overlayed over each other by automated or manual procedures, and the results were sent to the main form. re-slicing images were extracted from image data in the main form. In the re-slice form, the precise information of the brain region will be present in any new coordination system.

Fig. 2

The quality of pyRECaid application for Electrophysiological recording. The quality of neural data recording using pyRECaid software was evaluated after spike sorting in different depths for two recording chambers. a) In this panel the image coordination has changed over a chamber located on the prefrontal cortex. The panels in right show the quality of spiking activity was recorded. The yellowish line shows the sorted spikes in each panel. The distances were calculated from the top of the chamber for different depths: from −26 mm to −32 mm. The depth for each panel was written on the top of the panel. b) In this panel the image coordination has changed over the chamber located over the IT cortex. In this chamber, it is needed to penetrate electrodes in the angled view over the chamber. Similar to (a), right panels show the evaluation of software by recording in different depths. The distances were calculated form the base of manipulator in different depths: −52 mm to −61 mm.

Fig. 3

Pharmacological manipulation using pyRECaid software. The infusion cannula was inserted in six different locations of basal ganglia in two hemispheres. a) This panel shows the coronal section of cannula penetration to reach the posterior part of the caudate nucleus in both hemispheres. b) This panel shows the sagittal section of cannula penetration in order to reach the putamen and caudate in the left hemispheres. c) This panel shows the coordination for infusion in the putamen (+), anterior (o) and posterior (*) part of caudate. The coordination of all animals in one hemisphere was placed on the atlas’s coordination. d) Histology procedure for one animal in cell transplantation experiment. i-iv) Extracting putamen and caudate area from hole brain tissue. v-vi) Extracted target area (containing caudate and putamen) for left (v) and right (vi) hemispheres. e) Immunofluorescence staining of extracted target area. Representative images of double staining for the human cell marker Stem-121 (red) and a dopaminergic marker Tyrosine hydroxylase (TH, green) after six month of cell transplantation surgery. . (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 4

Planning human biopsy surgery using pyRECaid software. The software was verified in one patient after surgery compared to available commercial software (Inomed, Germany). a) Co-registration result for human data. CT imaging was done by surgical stereotaxic frame. b) The location of the tumor tissue in the MR image was located related to AC-PC line. c) Re-slice images over AC_PC line. d) The sagittal view of re-sliced image series parallel to AC-PC line.