A whole-brain monosynaptic input connectome to neuron classes in mouse visual cortex

Identification of structural connections between neurons is a prerequisite to understanding brain function. Here we developed a pipeline to systematically map brain-wide monosynaptic input connections to genetically defined neuronal populations using an optimized rabies tracing system. We used mouse visual cortex as the exemplar system and revealed quantitative target-specific, layer-specific and cell-class-specific differences in its presynaptic connectomes. The retrograde connectivity indicates the presence of ventral and dorsal visual streams and further reveals topographically organized and continuously varying subnetworks mediated by different higher visual areas. The visual cortex hierarchy can be derived from intracortical feedforward and feedback pathways mediated by upper-layer and lower-layer input neurons. We also identify a new role for layer 6 neurons in mediating reciprocal interhemispheric connections. This study expands our knowledge of the visual system connectomes and demonstrates that the pipeline can be scaled up to dissect connectivity of different cell populations across the mouse brain.

Regional, Layer, and Cell-Type-Specific Connectivity of the Mouse Default Mode Network

The evolutionarily conserved default mode network (DMN) is a distributed set of brain regions coactivated during resting states that is vulnerable to brain disorders. How disease affects the DMN is unknown, but detailed anatomical descriptions could provide clues. Mice offer an opportunity to investigate structural connectivity of the DMN across spatial scales with cell-type resolution. We co-registered maps from functional magnetic resonance imaging and axonal tracing experiments into the 3D Allen mouse brain reference atlas. We find that the mouse DMN consists of preferentially interconnected cortical regions. As a population, DMN layer 2/3 (L2/3) neurons project almost exclusively to other DMN regions, whereas L5 neurons project in and out of the DMN. In the retrosplenial cortex, a core DMN region, we identify two L5 projection types differentiated by in- or out-DMN targets, laminar position, and gene expression. These results provide a multi-scale description of the anatomical correlates of the mouse DMN.

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Mouse resting-state default mode network anatomy described at high resolution in 3D

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Systematic axon tracing shows cortical DMN regions are preferentially interconnected

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Layer 2/3 DMN neurons project mostly in the DMN; layer 5 neurons project in and out

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Retrosplenial cortex contains distinct types of in- and out-DMN projection neurons

A large-scale standardized physiological survey reveals functional organization of the mouse visual cortex

To understand how the brain processes sensory information to guide behavior, we must know how stimulus representations are transformed throughout the visual cortex. Here we report an open, large-scale physiological survey of activity in the awake mouse visual cortex: the Allen Brain Observatory Visual Coding dataset. This publicly available dataset includes the cortical activity of nearly 60,000 neurons from six visual areas, four layers, and 12 transgenic mouse lines in a total of 243 adult mice, in response to a systematic set of visual stimuli. We classify neurons on the basis of joint reliabilities to multiple stimuli and validate this functional classification with models of visual responses. While most classes are characterized by responses to specific subsets of the stimuli, the largest class is not reliably responsive to any of the stimuli and becomes progressively larger in higher visual areas. These classes reveal a functional organization wherein putative dorsal areas show specialization for visual motion signals.

Aberration-free multi-plane imaging of neural activity from the mammalian brain using a fast-switching liquid crystal spatial light modulator

We report a novel two-photon fluorescence microscope based on a fast-switching liquid crystal spatial light modulator and a pair of galvo-resonant scanners for large-scale recording of neural activity from the mammalian brain. The spatial light modulator is used to achieve fast switching between different imaging planes in multi-plane imaging and correct for intrinsic optical aberrations associated with this imaging scheme. The utilized imaging technique is capable of monitoring the neural activity from large populations of neurons with known coordinates spread across different layers of the neocortex in awake and behaving mice, regardless of the fluorescent labeling strategy. During each imaging session, all visual stimulus driven somatic activity could be recorded in the same behavior state. We observed heterogeneous response to different types of visual stimuli from ∼ 3,300 excitatory neurons reaching from layer II/III to V of the striate cortex.

Whole brain imaging reveals distinct spatial patterns of amyloid beta deposition in three mouse models of Alzheimer's disease

A variety of Alzheimer's disease (AD) mouse models overexpress mutant forms of human amyloid precursor protein (APP), producing high levels of amyloid β (Aβ) and forming plaques. However, the degree to which these models mimic spatiotemporal patterns of Aβ deposition in brains of AD patients is unknown. Here, we mapped the spatial distribution of Aβ plaques across age in three APP-overexpression mouse lines (APP/PS1, Tg2576, and hAPP-J20) using in vivo labeling with methoxy-X04, high throughput whole brain imaging, and an automated informatics pipeline. Images were acquired with high resolution serial two-photon tomography and labeled plaques were detected using custom-built segmentation algorithms. Image series were registered to the Allen Mouse Brain Common Coordinate Framework, a 3D reference atlas, enabling automated brain-wide quantification of plaque density, number, and location. In both APP/PS1 and Tg2576 mice, plaques were identified first in isocortex, followed by olfactory, hippocampal, and cortical subplate areas. In hAPP-J20 mice, plaque density was highest in hippocampal areas, followed by isocortex, with little to no involvement of olfactory or cortical subplate areas. Within the major brain divisions, distinct regions were identified with high (or low) plaque accumulation; for example, the lateral visual area within the isocortex of APP/PS1 mice had relatively higher plaque density compared with other cortical areas, while in hAPP-J20 mice, plaques were densest in the ventral retrosplenial cortex. In summary, we show how whole brain imaging of amyloid pathology in mice reveals the extent to which a given model recapitulates the regional Aβ deposition patterns described in AD.

An anatomic transcriptional atlas of human glioblastoma

Glioblastoma is an aggressive brain tumor that carries a poor prognosis. The tumor's molecular and cellular landscapes are complex, and their relationships to histologic features routinely used for diagnosis are unclear. We present the Ivy Glioblastoma Atlas, an anatomically based transcriptional atlas of human glioblastoma that aligns individual histologic features with genomic alterations and gene expression patterns, thus assigning molecular information to the most important morphologic hallmarks of the tumor. The atlas and its clinical and genomic database are freely accessible online data resources that will serve as a valuable platform for future investigations of glioblastoma pathogenesis, diagnosis, and treatment.

Exploration and visualization of connectivity in the adult mouse brain

The Allen Mouse Brain Connectivity Atlas is a mesoscale whole brain axonal projection atlas of the C57Bl/6J mouse brain. All data were aligned to a common template in 3D space to generate a comprehensive and quantitative database of inter-areal and cell-type-specific projections. A suite of computational tools were developed to search and visualize the projection labeling experiments, available at http://connectivity.brain-map.org. We present three use cases illustrating how these publicly-available tools can be used to perform analyses of long range brain region connectivity. The use cases make extensive use of advanced visualization tools integrated with the atlas including projection density histograms, 3D computed anterograde and retrograde projection paths, and multi-specimen projection composites. These tools offer convenient access to detailed axonal projection information in the adult mouse brain and the ability to perform data analysis and visualization of projection fields and neuroanatomy in an integrated manner.

Neuroinformatics of the Allen Mouse Brain Connectivity Atlas

The Allen Mouse Brain Connectivity Atlas is a mesoscale whole brain axonal projection atlas of the C57Bl/6J mouse brain. Anatomical trajectories throughout the brain were mapped into a common 3D space using a standardized platform to generate a comprehensive and quantitative database of inter-areal and cell-type-specific projections. This connectivity atlas has several desirable features, including brain-wide coverage, validated and versatile experimental techniques, a single standardized data format, a quantifiable and integrated neuroinformatics resource, and an open-access public online database (http://connectivity.brain-map.org/). Meaningful informatics data quantification and comparison is key to effective use and interpretation of connectome data. This relies on successful definition of a high fidelity atlas template and framework, mapping precision of raw data sets into the 3D reference framework, accurate signal detection and quantitative connection strength algorithms, and effective presentation in an integrated online application. Here we describe key informatics pipeline steps in the creation of the Allen Mouse Brain Connectivity Atlas and include basic application use cases.

A high-resolution spatiotemporal atlas of gene expression of the developing mouse brain

To provide a temporal framework for the genoarchitecture of brain development, we generated in situ hybridization data for embryonic and postnatal mouse brain at seven developmental stages for ∼2,100 genes, which were processed with an automated informatics pipeline and manually annotated. This resource comprises 434,946 images, seven reference atlases, an ontogenetic ontology, and tools to explore coexpression of genes across neurodevelopment. Gene sets coinciding with developmental phenomena were identified. A temporal shift in the principles governing the molecular organization of the brain was detected, with transient neuromeric, plate-based organization of the brain present at E11.5 and E13.5. Finally, these data provided a transcription factor code that discriminates brain structures and identifies the developmental age of a tissue, providing a foundation for eventual genetic manipulation or tracking of specific brain structures over development. The resource is available as the Allen Developing Mouse Brain Atlas (http://developingmouse.brain-map.org).

Large-scale cellular-resolution gene profiling in human neocortex reveals species-specific molecular signatures

Although there have been major advances in elucidating the functional biology of the human brain, relatively little is known of its cellular and molecular organization. Here we report a large-scale characterization of the expression of ∼1,000 genes important for neural functions by in situ hybridization at a cellular resolution in visual and temporal cortices of adult human brains. These data reveal diverse gene expression patterns and remarkable conservation of each individual gene's expression among individuals (95%), cortical areas (84%), and between human and mouse (79%). A small but substantial number of genes (21%) exhibited species-differential expression. Distinct molecular signatures, comprised of genes both common between species and unique to each, were identified for each major cortical cell type. The data suggest that gene expression profile changes may contribute to differential cortical function across species, and in particular, a shift from corticosubcortical to more predominant corticocortical communications in the human brain.

Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain

BACKGROUND

Spatially mapped large scale gene expression databases enable quantitative comparison of data measurements across genes, anatomy, and phenotype. In most ongoing efforts to study gene expression in the mammalian brain, significant resources are applied to the mapping and visualization of data. This paper describes the implementation and utility of Brain Explorer, a 3D visualization tool for studying in situ hybridization-based (ISH) expression patterns in the Allen Brain Atlas, a genome-wide survey of 21,000 expression patterns in the C57BL\6J adult mouse brain.

RESULTS

Brain Explorer enables users to visualize gene expression data from the C57Bl/6J mouse brain in 3D at a resolution of 100 microm3, allowing co-display of several experiments as well as 179 reference neuro-anatomical structures. Brain Explorer also allows viewing of the original ISH images referenced from any point in a 3D data set. Anatomic and spatial homology searches can be performed from the application to find data sets with expression in specific structures and with similar expression patterns. This latter feature allows for anatomy independent queries and genome wide expression correlation studies.

CONCLUSION

These tools offer convenient access to detailed expression information in the adult mouse brain and the ability to perform data mining and visualization of gene expression and neuroanatomy in an integrated manner.

The conditional binomial test revisited for clinical trials

McNemar's test is used to test the hypothesis that one treatment is better than another in a matched-pair design for binary outcomes. The conditional binomial test in such a matched-pair design is the exact McNemar test. However, in many clinical trials, one wants to establish equivalency between two treatments. We discuss how to use a conditional binomial test to establish equivalency between two treatments in a matched-pair design. Sample size and power determination for each conditional binomial test are calculated. Some statistical properties of the tests are analyzed through Monte Carlo simulation.

A feasibility study of the AutoPap system location-guided screening

OBJECTIVE

To study the feasibility of AutoPap System location-guided screening and to evaluate the accuracy of the AutoPap System in selecting locations of potentially abnormal cellular material, the accuracy of triaging slides using the selected locations and the improvement in laboratory accuracy and workload reduction resulting from a combination of location-guided rescreening and AutoPap System primary screening.

STUDY DESIGN

For the study, 683 conventionally prepared cervical cytologic smears (263 WNL, 184 atypical squamous cells of undetermined significance/atypical glandular cells of undetermined significance, 173 low grade squamous intraepithelial lesions, 55 high grade squamous intraepithelial lesions and 8 cancer slides) were acquired from nine laboratories. The study slides were independently screened to establish study reference diagnoses. The slides were processed on the AutoPap System and screened by cytotechnologists who were guided by the field of view (FOV) locations provided by the AutoPap System. The location-guided information was used either for initial manual screening (location-guided screening or after initial manual screening of the entire slide (location-guided rescreening). The results were compared to the study reference diagnoses. Sensitivity and workload reduction figures were estimated for different slide populations.

RESULTS

The accuracy of location-guided slide triage was high and did not vary significantly over different slide populations. Also, for > 80% of the abnormal slides, the AutoPap System-selected FOV slide locations did contain the most diagnostic cells, which were used to assign an accurate diagnosis to the slide. By combining location-guided rescreening with AutoPap primary screening, the estimated overall location-guided screening false negative fraction (FNF) for LSIL+ slides was approximately 40 times lower than the cytotechnologist-only FNFs, and this improvement was achieved-even at a no review rate of 70%.

CONCLUSION

The feasibility study results showed that the AutoPap System location-guided screening process can triage slides accurately and enhance the overall accuracy of slide diagnosis. The combination of location-guided rescreening and AutoPap primary screening could improve the accuracy and workload of the laboratory.

Effectiveness of automated cervical cytology rescreening using the AutoPap 300 QC System

This study assesses the performance of the AutoPap 300 QC System in identifying false-negative (FN) smears in a slide population previously screened as normal and compares the detection rate to that achieved with a random rescreen of the same slide population. A total of 1,840 "normal" smears were rescreened both manually and by the AutoPap 300 QC System. Overall, a total of 7 FN slides were detected. At QC selection rates of 30% and 20% the device achieved sensitivities for detection of FN smears of 57.19% (4/7) and 42.8% (3/7), respectively. This represents a three- to fourfold enrichment in the number of FN smears over that obtained by a random rescreen of a similar proportion of cases. None of the FN slides were identified by either method at a 10% rescreening rate. The ability of the device to detect slides previously classified as abnormal (n = 139) and FN (n = 40) was also studied. The overall sensitivity to abnormal smears at QC selection rates of 10%, 20%, and 50% was 61.9%, 77.0%, and 94.2%, respectively. Improved sensitivity to smears classified as LSIL or worse (n = 112) was obtained for corresponding selection rates (61.6%, 75.9%, and 93.8%). Sensitivity to FN slides classified as LSIL or worse (n = 17) for QC selection rates of 10%, 20%, and 50% was 29.4%, 70.6%, and 88.2%, respectively. The sensitivity and specificity of the device to an adequate squamous and endocervical cell component was also determined. At predetermined thresholds, the overall sensitivity to slides with an inadequate squamous cell component (n = 55) and to those smears with an endocervical cell component (n = 1.587) was 81.8%, and 82.7% respectively. The study demonstrated that the AutoPap 300 QC System is superior to human random rescreen for the identification of FN smears although only a marginal improvement was noted due to the small sample. Further studies are required using a larger number of smears to fully assess the value of the device in quality control mode. The device also has the potential to improve the accuracy of specimen adequacy determinations and to serve as a useful adjunct to existing quality control measures designed to monitor individual performance and reporting accuracy.

AutoPap system performance in screening for low prevalence and small cell abnormalities

OBJECTIVE

To summarize the design principles of the AutoPap System evaluation score by evaluating slides having a low prevalence of abnormal cells and small cell abnormalities and assessing the evaluation score as a diagnostic tool.

STUDY DESIGN

Data from two clinical studies conducted using the AutoPap System and data obtained from the evaluation score training slides were analyzed to demonstrate the effectiveness of the evaluation score. The clinical studies included a prospective, intended-use study involving approximately 13,000 slides and a comprehensive sensitivity study using approximately 1,200 slides from five laboratories. The evaluation score training set consisted of 4,174 slides from 10 laboratories.

RESULTS

The robust design of the AutoPap evaluation score was demonstrated by similar detection capabilities and sensitivities to slides having either a low or high prevalence of abnormal cells. No significant difference in performance was detected between the small cell slides and the comparison groups of carcinoma in situ and invasive squamous carcinoma having normal-sized abnormal cells. In addition, the evaluation scores corresponded well to the diagnostic severity of the slides.

Grading cervical dysplasia with AgNORs using a semiautomated image analysis system

Colposcopic biopsies were classified according to previously established criteria by a group of three pathologists interested in cervical pathology. Ten cases were identified in each of the following five groups: normal, koilocytosis, low grade squamous intraepithelial lesions (CIN 1), high grade squamous intraepithelial lesions (CIN 2) and high grade squamous intraepithelial lesions (CIN 3). The Crocker technique was used to stain the sections cut 3 microns thick. With ths silver stain the nucleolar organizer regions (NORs) are stained black and referred to as AgNORs. It has been shown that malignant and premalignant changes in cells produce an increase in AgNORs. In each case eight images were captured using a 100x oil-immersion objective and stored in a Datacube Maxvideo system as 512 x 480 pixels in an 8-bit grayscale per image. The images were processed using the NeoPath field-of-view computer to detect the AgNORs and nuclei by using grayscale mathematical morphology algorithms. Color overlays of the AgNORs and nuclei were created using segmentation algorithms. The results show that it is possible to differentiate between low grade squamous intraepithelial lesions (CIN 1) and high grade squamous intraepithelial lesions (CIN 2 and CIN 3) taken together; however, there is no difference between low grade squamous intraepithelial lesions (CIN 1) and koilocytosis. The results support the concept that dysplasia cannot be classified effectively into three grades and that low grade squamous intraepithelial lesions (mild dysplasia [CIN 1]) is indistinguishable from koilocytosis.