Primatologist: A modular segmentation pipeline for macaque brain morphometry

Balbastre, Yaël; Rivière, Denis; Souedet, Nicolas; Fischer, Clara; Hérard, Anne‐Sophie; Williams, Susannah; Vandenberghe, Michel; Flament, Julien; Aron-Badin, Romina; Hantraye, Philippe; Mangin, Jean‐François; Delzescaux, Thierry

doi:10.1016/j.neuroimage.2017.09.007

Cited by 14 publications

(18 citation statements)

References 86 publications

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“…This dataset is distributed under the CeCILLv2.1 license ( http://www.cecill.info ), a GPL-compatible license, and can be freely used for academic work, upon citing this paper. This dataset was used to validate automated segmentations obtained with Primatologist, a pipeline dedicated to macaque brain morphology analysis [2] . The list of provided files is summarized in Table 1 .…”

Section: Datamentioning

confidence: 99%

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A validation dataset for Macaque brain MRI segmentation

et al. 2018

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Validation data for segmentation algorithms dedicated to preclinical images is fiercely lacking, especially when compared to the large number of databases of Human brain images and segmentations available to the academic community. Not only is such data essential for validating methods, it is also needed for objectively comparing concurrent algorithms and detect promising paths, as segmentation challenges have shown for clinical images.The dataset we present here is a first step in this direction. It comprises 10 T2-weighted MRIs of healthy adult macaque brains, acquired on a 7 T magnet, along with corresponding manual segmentations into 17 brain anatomic labelled regions spread over 5 hierarchical levels based on a previously published macaque atlas (Calabrese et al., 2015) [1].By giving access to this unique dataset, we hope to provide a reference needed by the non-human primate imaging community. This dataset was used in an article presenting a new primate brain morphology analysis pipeline, Primatologist (Balbastre et al., 2017) [2]. Data is available through a NITRC repository (https://www.nitrc.org/projects/mircen_macset).

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Section: Datamentioning

confidence: 99%

“…By giving access to this unique dataset, we hope to provide a reference needed by the non-human primate imaging community. This dataset was used in an article presenting a new primate brain morphology analysis pipeline, Primatologist (Balbastre et al, 2017) [2] . Data is available through a NITRC repository ( https://www.nitrc.org/projects/mircen_macset ).…”

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A validation dataset for Macaque brain MRI segmentation

et al. 2018

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“…For instance, because they reside on a laboratory's internal servers or personal websites. However, people's attitudes towards openly sharing the resource solutions they have developed appears to be improving (Balbastre et al, 2017;Tasserie et al, 2020) and new developments in information technology promote such initiatives while simultaneously creating avenues to assign explicit credit to…”

Section: Discussionmentioning

confidence: 99%

“…The field of human neuroimaging has started to address these issues with initiatives for standardized, reproducible analysis pipelines (BIDS, Nipype, etc) (Gorgolewski et al, 2011(Gorgolewski et al, , 2016, data sharing (OpenfMRI, Zenodo, Neurovault, etc) (Gorgolewski et al, 2015;Poldrack et al, 2013), and collaborative and open coding (GitHub, GitLab, etc). NHP neuroimaging has been lagging behind in adopting such collaborative open science initiatives, but people's willingness to share and be open about the resource solutions they developed is steadily increasing (Balbastre et al, 2017;Tasserie et al, 2020) and new developments in information technology promote these initiatives, while creating avenues to assign explicit credit to developers. The global NHP neuroimaging consortium (Milham et al, 2020(Milham et al, , 2018…”

Section: Introductionmentioning

confidence: 99%

A collaborative resource platform for non-human primate neuroimaging

Messinger¹,

Sirmpilatze

Heuer

et al. 2020

Preprint

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Neuroimaging non-human primates (NHPs) is a growing, yet highly specialized field of neuroscience. Resources that were primarily developed for human neuroimaging often need to be significantly adapted for use with NHPs or other animals, which has led to an abundance of custom, in-house solutions. In recent years, the global NHP neuroimaging community has made significant efforts to transform the field towards more open and collaborative practices. Here we present the PRIMatE Resource Exchange (PRIME-RE), a new collaborative online platform for NHP neuroimaging. PRIME-RE is a dynamic community-driven hub for the exchange of practical knowledge, specialized analytical tools, and open data repositories, specifically related to NHP neuroimaging. PRIME-RE caters to both researchers and developers who are either new to the field, looking to stay abreast of the latest developments, or seeking to collaboratively advance the field.

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“…Collected time frames were summed to create an integrated image for manual co-registration with the T2-weighted MRI using an in-house anatomo-functional image processing software (Anatomist; http:// www.brainvisa.info) and a dedicated PMOD software (PMOD Technologies). Anatomical regions of interest (ROI) were automatically delineated on the putamen and caudate nuclei, the IHC regions (see $2.6.2) and cortical/subcortical regions on individual MRI images using the CIVM atlas and the Primatologist segmentation pipeline for the macaque brain (Balbastre et al, 2017). After T2-MRI and PET-co-registration, the mean activity of each ROI was extracted from the dynamic PET data as a TAC.…”

Section: Pet Image Analysismentioning

confidence: 99%

Longitudinal characterization of cognitive and motor deficits in an excitotoxic lesion model of striatal dysfunction in non-human primates

Lavisse

Williams

Sophie

et al. 2019

Neurobiology of Disease

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As research progresses in the understanding of the molecular and cellular mechanisms underlying neurodegenerative diseases like Huntington's disease (HD) and expands towards preclinical work for the development of new therapies, highly relevant animal models are increasingly needed to test new hypotheses and to validate new therapeutic approaches. In this light, we characterized an excitotoxic lesion model of striatal dysfunction in non-human primates (NHPs) using cognitive and motor behaviour assessment as well as functional imaging and post-mortem anatomical analyses. NHPs received intra-striatal stereotaxic injections of quinolinic acid bilaterally in the caudate nucleus and unilaterally in the left sensorimotor putamen. Post-operative MRI scans showed atrophy of the caudate nucleus and a large ventricular enlargement in all 6 NHPs that correlated with post-mortem measurements. Behavioral analysis showed deficits in 2 analogues of the Wisconsin card sorting test (perseverative behavior) and in an executive task, while no deficits were observed in a visual recognition or an episodic memory task at 6 months following surgery. Spontaneous locomotor activity was decreased after lesion and the incidence of apomorphine-induced dyskinesias was significantly increased at 3 and 6 months following lesion. Positron emission tomography scans obtained at end-point showed a major deficit in glucose metabolism and D2 receptor density limited to the lesioned striatum of all NHPs compared to controls. Post-mortem analyses revealed a significant loss of medium-sized spiny neurons in the striatum, a loss of neurons and fibers in the globus pallidus, a unilateral decrease in dopaminergic neurons of the substantia nigra and a loss of neurons in the motor and dorsolateral prefrontal cortex. Overall, we show that this robust NHP model presents specific behavioral (learning, execution and retention of cognitive tests) and metabolic functional deficits that, to the best of our knowledge, are currently not mimicked in any available large animal model of striatal dysfunction. Moreover, we used non-invasive, translational techniques like behavior and imaging to quantify such deficits and found that they correlate to a significant cell loss in the striatum and its main input and output structures. This model can thus significantly contribute to the pre-clinical longitudinal evaluation of the ability of new therapeutic cell, gene or pharmacotherapy approaches in restoring the functionality of the striatal circuitry.

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Primatologist: A modular segmentation pipeline for macaque brain morphometry

Cited by 14 publications

References 86 publications

A validation dataset for Macaque brain MRI segmentation

A validation dataset for Macaque brain MRI segmentation

A collaborative resource platform for non-human primate neuroimaging

Longitudinal characterization of cognitive and motor deficits in an excitotoxic lesion model of striatal dysfunction in non-human primates

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