Nutil: A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images

Groeneboom, N. E.; Yates, Sharon; Puchades, Maja; Bjaalie, Jan G.

doi:10.3389/fninf.2020.00037

Cited by 50 publications

(50 citation statements)

References 22 publications

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“…The trained object classifier was then batch applied to the remainder of the brain sections from that animal, and the resulting object segmentations were exported for each section. The custom atlas maps of each brain section and the object segmentations were combined in the Nutil Quantifier application (Groeneboom et al, 2020;Yates et al, 2019), returning object counts for each atlas brain region. This process was repeated separately for each animal.…”

Section: Image Analysismentioning

confidence: 99%

The synaptic inputs and thalamic projections of two classes of layer 6 corticothalamic neurons in primary somatosensory cortex of the mouse

Whilden

Chevée

et al. 2021

J of Comparative Neurology

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Although corticothalamic neurons (CThNs) represent the largest source of synaptic input to thalamic neurons, their role in regulating thalamocortical interactions remains incompletely understood. CThNs in sensory cortex have historically been divided into two types, those with cell bodies in Layer 6 (L6) that project back to primary sensory thalamic nuclei and those with cell bodies in Layer 5 (L5) that project to higher-order thalamic nuclei and subcortical structures. Recently, diversity among L6 CThNs has increasingly been appreciated. In the rodent somatosensory cortex, two major classes of L6 CThNs have been identified: one projecting to the ventral posterior medial nucleus (VPM-only L6 CThNs) and one projecting to both VPM and the posterior medial nucleus (VPM/POm L6 CThNs). Using rabies-based tracing methods in mice, we asked whether these L6 CThN populations integrate similar synaptic inputs. We found that both types of L6 CThNs received local input from somatosensory cortex and thalamic input from VPM and POm. However, VPM/POm L6 CThNs received significantly more input from a number of additional cortical areas, higher order thalamic nuclei, and subcortical structures. We also found that the two types of L6 CThNs target different functional regions within the thalamic reticular nucleus (TRN). Together, our results indicate that these two types of L6 CThNs represent distinct information streams in the somatosensory cortex and suggest that VPM-only L6 CThNs regulate, via their more restricted circuits, sensory responses related to a cortical column while VPM/POm L6 CThNs, which are integrated into more widespread POm-related circuits, relay contextual information.

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Section: Image Analysismentioning

confidence: 99%

The synaptic inputs and thalamic projections of two classes of layer 6 corticothalamic neurons in primary somatosensory cortex of the mouse

Whilden

Chevée

et al. 2021

J of Comparative Neurology

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“…Immunohistochemical techniques continue to serve important purposes for characterizing cell populations based on protein expression (which may only be a subset of those expressing the gene for the protein). To achieve efficient quantification of immunohistochemically labeled cells in sectioned material, we used the QUINT workflow ( Yates et al., 2019 ), which combines three open-access tools, QuickNII ( Puchades et al., 2019 ), ilastik ( Berg et al., 2019 ), and Nutil ( Groeneboom et al., 2020 ). This workflow achieves quantification of segmented objects in atlas-defined regions of interest, using customized brain atlas maps, section coordinates, and machine-learning-based segmentation of the labeled objects.…”

Section: Introductionmentioning

confidence: 99%

Densities and numbers of calbindin and parvalbumin positive neurons across the rat and mouse brain

et al. 2021

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Summary The calcium-binding proteins parvalbumin and calbindin are expressed in neuronal populations regulating brain networks involved in spatial navigation, memory processes, and social interactions. Information about the numbers of these neurons across brain regions is required to understand their functional roles but is scarcely available. Employing semi-automated image analysis, we performed brain-wide analysis of immunohistochemically stained parvalbumin and calbindin sections and show that these neurons distribute in complementary patterns across the mouse brain. Parvalbumin neurons dominate in areas related to sensorimotor processing and navigation, whereas calbindin neurons prevail in regions reflecting behavioral states. We also find that parvalbumin neurons distribute according to similar principles in the hippocampal region of the rat and mouse brain. We validated our results against manual counts and evaluated variability of results among researchers. Comparison of our results to previous reports showed that neuron numbers vary, whereas patterns of relative densities and numbers are consistent.

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“…We chose to employ QuickNII (Puchades et al, 2019) as it requires minimal user-guided manual transformations, does not introduce distortions in the original experimental images, and provides AMB coordinates for each experimental image to facilitate the registration of segmented objects (i.e. microspheres) to anatomical structures (Groeneboom et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

“…This step is necessary for determining which hemisphere (right vs. left) the microsphere is located in. Subsequently, the precise location of each microsphere was determined by utilizing the complementary software Nutil (Groeneboom et al, 2020). Nutil utilizes the AMB spatial coordinates of the block-face images obtained from QuickNII and combines it with the binary segmentation masks of your objects of interest (i.e.…”

Section: Alignment To Allen Mouse Brain Atlasmentioning

confidence: 99%

Localizing Microemboli within the Rodent Brain through Block-Face Imaging and Atlas Registration

McDonald

Jeffers

Filadelfi

et al. 2021

eNeuro

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Brain microinfarcts are prevalent in humans, however due to the inherent difficulty of identifying and localizing individual microinfarcts, brain-wide quantification is impractical. In mice, microinfarcts have been created by surgically introducing microemboli into the brain, but a major limitation of this model is the absence of automated methods to identify and localize individual occlusions. We present a novel and semi-automated workflow to identify the anatomical location of fluorescent emboli (microspheres) within the mouse brain through histological processing and atlas registration. By incorporating vibratome block-face imaging with the QuickNII brain registration tool, we show that the anatomical location of microspheres can be accurately registered to brain structures within the Allen mouse brain (AMB) atlas (e.g. somatomotor areas, hippocampal region, visual areas, etc.). Compared to registering images of slide mounted sections to the AMB atlas, microsphere location was more accurately determined when block-face images were utilized. As a proof of principle, using this workflow we compared the distribution of microspheres within the brains of mice that were either perfused or immersion fixed. No significant effect of perfusion on total microsphere number or location was detected. In general, microspheres were distributed brain-wide, with the largest density found in the thalamus. In sum, our block-face imaging workflow, enables efficient characterization of the widespread distribution of fluorescent microemboli, facilitating future investigation into the impact of microinfarct load and location on brain health. Significance StatementCerebral microemboli are small materials, such as a blood clot or atherosclerotic plaque, that pass through the circulation until being lodged within downstream vasculature and occasionally resulting in localized cell death (microinfarction). The largest limitation of microemboli models of microinfarction in rodents is the lack of efficient methods for accurately quantifying the brainwide distribution of occlusions in individual subjects. Compared to traditional histology, incorporating our block-face imaging workflow significantly reduces the time required to register all emboli from a single brain (from days to hours). Going forward, this workflow will allow researchers to more efficiently characterize the global distribution of microemboli in mice and facilitate the stratification of mice based on microsphere load or location.

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Nutil: A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images

Cited by 50 publications

References 22 publications

The synaptic inputs and thalamic projections of two classes of layer 6 corticothalamic neurons in primary somatosensory cortex of the mouse

The synaptic inputs and thalamic projections of two classes of layer 6 corticothalamic neurons in primary somatosensory cortex of the mouse

Densities and numbers of calbindin and parvalbumin positive neurons across the rat and mouse brain

Localizing Microemboli within the Rodent Brain through Block-Face Imaging and Atlas Registration

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