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PubMed2025

Spatial mutual nearest neighbors for spatial transcriptomics data.

MOTIVATION: Mutual nearest neighbors (MNN) is a widely used computational tool to perform batch correction for single-cell RNA-sequencing data. However, in applications such as spatial transcriptomics, it fails to take into account the 2D spatial information. RESULTS: Here, we present spatialMNN, an algorithm that integrates multiple spatial transcriptomic samples and identifies spatial domains. Our approach begins by building a k-nearest neighbors (kNN) graph based on the spatial coordinates, prunes noisy edges, and identifies niches to act as anchor points for each sample. Next, we construct a MNN graph across the samples to identify similar niches. Finally, the spatialMNN graph can be partitioned using existing algorithms, such as the Louvain algorithm to predict spatial domains across the tissue samples. We demonstrate the performance of spatialMNN using large datasets, including one with N = 31 10x Genomics Visium samples. We also evaluate the computing performance of spatialMNN to other popular spatial clustering methods. AVAILABILITY AND IMPLEMENTATION: Our software package is available on GitHub (https://github.com/Pixel-Dream/spatialMNN). The code is available on Zenodo (https://doi.org/10.5281/zenodo.15073963).

Algorithms↗

PubMed2026

SIVA: diagonal integration of spatial multi-omics data via spatially informed variational autoencoders and anchor guidance.

MOTIVATION: Understanding cellular states and regulatory programs requires integrative analysis of multiple omics layers. Although recent spatial sequencing technologies allow molecular profiling of cells within their tissue context, paired spatial multi-omics assays are still limited by technical complexity and cost. This creates a pressing need for diagonal integration methods that enable joint analysis of unpaired spatial omics datasets. RESULTS: We propose SIVA, a deep generative framework based on Spatially-Informed Variational Autoencoders with Anchor Guidance, for diagonal integration of spatial multi-modal data. SIVA employs modality-specific variational autoencoders (VAEs) with a hybrid latent embedding that integrates Gaussian process and standard Gaussian priors, enabling joint modeling of spatially structured variation and dominant underlying data distributions across modalities. To facilitate cross-modal alignment in the absence of one-to-one cell correspondence, SIVA adopts a dual integration strategy combining global distribution alignment via Maximum Mean Discrepancy and local correspondence guidance using mutual nearest neighbor anchors. Extensive experiments across multiple cross-slice integration scenarios demonstrate that SIVA achieves robust and accurate integration of unpaired spatial omics datasets, consistently outperforming existing methods. AVAILABILITY AND IMPLEMENTATION: The source codes are available at https://github.com/PelenJiang/SIVA.

Autoencoder↗

PubMed1990

The effects of temporal modulation and spatial location on the perceived spatial frequency of visual patterns.

The perceived spatial frequency of a visual pattern can increase when a pattern drifts or is presented at a peripheral visual field location, as compared with a foveally viewed, stationary pattern. We confirmed previously reported effects of motion on foveally viewed patterns and of location on stationary patterns and extended this analysis to the effect of motion on peripherally viewed patterns and the effect of location on drifting patterns. Most central to our investigation was the combined effect of temporal modulation and spatial location on perceived spatial frequency. The group data, as well as the individual sets of data for most observers, are consistent with the mathematical concept of separability for the effects of temporal modulation and spatial location on perceived spatial frequency. Two qualitative psychophysical models suggest explanations for the effects. Both models assume that the receptive-field sizes of a set of underlying psychophysical mechanisms monotonically change as a function of temporal modulation or visual field location, whereas the perceptual labels attached to a set of channels remain invariant. These models predict that drifting or peripheral viewing of a pattern will cause a shift in the perceived spatial frequency of the pattern to a higher apparent spatial frequency.

Adult↗

PubMed1990

The effects of spatial phase on reaction time to spatially filtered images.

Many studies of visual perception have used periodic stimuli such as sine-wave gratings and checkerboard patterns. It is well known that reaction time (RT) to such stimuli increases with increasing spatial frequency and decreasing contrast. While this is the case with periodic stimuli it is not clear that these relationships obtain for aperiodic stimuli such as natural scenes. A digitized image of an object (a vase) was submitted to two-dimensional Fourier analysis. Four pairs of spatial frequency band-limited images were created for each image. Each pair consisted of a normal-phase (NP) and a scrambled-phase (SP) version, with the magnitude spectrum and space-averaged luminance the same within each pair. Filter band-widths were 1 octave wide. Manual RT was measured for onset and offset of each spatially filtered image. Mean RT for SP images increased significantly with increasing spatial frequency, while no other significant differences were found with the NP images. This suggests that the temporal processing of complex, aperiodic images is influenced by the spatial frequency and contrast of local regions within the image, rather than by the space-averaged contrast of the entire image, and cannot be predicted by global estimates of contrast and spatial frequency.

Adult↗

PubMed1992

Spatial recognition and spatial order memory in patients with dementia of the Alzheimer's type.

Patients diagnosed as having mild or moderate primary degenerative dementia of the Alzheimer's type (PDDAT), and normal elderly subjects were tested for spatial order and a spatial recognition memory. Results for spatial order memory indicated that compared to normal elderly subjects, patients with mild PDDAT showed an impaired memory only for the last serial positions. In contrast, with respect to spatial recognition memory, patients with mild PDDAT showed an impaired memory only for the early serial positions. Patients with moderate PDDAT were impaired on all serial positions for both spatial order and spatial recognition memory. Based on comparable deficit patterns seen in animals and patients with hippocampal and parietal cortex lesions, it is suggested that memory deficits displayed by PDDAT patients might be a function of underlying pathology in the hippocampus and parietal cortex.

Aged↗

PubMed1988

Spatial frequency and orientation tuning of spatial visual mechanisms in human albinos.

A masking paradigm was used to measure the spatial frequency and orientation tuning of spatial mechanisms in the albino visual system. Threshold elevation curves obtained in this manner at test spatial frequencies of 0.25 cycles/deg (cpd), 0.50 cpd, and 1 cpd have the same shape as curves obtained from normal subjects at test frequencies two octaves higher. Additional masking studies showed that contrast processing in albinos obeys the same compressive power law as in normals. Thus, spatial mechanisms in albino central vision have normal spatial frequency and orientation bandwidths. As central cones in the albino are spaced 3-4 times further apart than in the normal fovea, these results support the hypothesis that monocular spatial vision in albinos is primarily limited by this increased receptor spacing. It is hypothesized that this, in turn, is the result of arrested development of the albino retina.

Adult↗

PubMed1988

Sex differences in the lateralization of spatial abilities: a spatial component analysis of extreme group scores.

Sex differences in the cerebral lateralization of two discrete components of spatial processing were investigated in high and low ability males and females using the dual-task paradigm. In the first phase of the experiment, the results indicated a pattern of right hemispheric control for a spatial visualization component, regardless of sex and ability level. In the processing of the spatial orientation component of spatial ability, high ability males and females showed left hemispheric lateralization, whereas low ability males and females displayed right hemispheric control. In the second phase of this study, it was observed that high ability females and low ability males may use a verbal mediation strategy in processing spatial visualization tasks. No verbal mediation effects were found for the spatial orientation component.

Adult↗

PubMed1989

Spatial summation of heat-induced pain: influence of stimulus area and spatial separation of stimuli on perceived pain sensation intensity and unpleasantness.

1. Psychophysical experiments were initiated to determine the possible influence of increasing stimulus size on perceived pain intensity. Six trained human subjects (5 male, 1 female) made visual analogue scale (VAS) ratings for pain-sensation intensity and unpleasantness in response to nociceptive thermal stimuli. Test stimuli consisted of 5-s duration heat pulses (45-50 degrees C in 1 degrees increments) delivered by one, two, or three contact thermal probes (1 cm2 each) applied to the medial aspect of the anterior forearm. 2. The area of skin receiving noxious thermal stimuli was changed by randomly varying the number of thermodes activated. The effects of varying the distance between the thermal probes also were evaluated. In the first series of experiments, thermal-probe separation was kept close to 0; in subsequent experimental series, the thermodes were separated by either 5 or 10 cm. 3. In each experimental series, considerable spatial summation occurred in both pain-sensation intensity and unpleasantness dimensions of pain. This summation occurred throughout the nociceptive thermal range of 45-50 degrees C and was larger at suprathreshold temperatures (greater than or equal to 47 degrees C) than those near threshold (less than or equal to 46 degrees C). Unlike spatial summation of perceived warmth, that of pain was not characterized by systematic changes in power-function exponents but as approximately upward parallel displacements in double-logarithmic coordinates. 4. Thermal-probe separation over a range of 0-10 cm had no effects on spatial summation of pain-sensation intensity or pain unpleasantness. In contrast, increasing thermal-probe separation increased the subjects' ability to discriminate differences in stimulus size and their ability to detect correctly the number of thermal probes activated. 5. Because affective VAS ratings of unpleasantness were linearly related to, but distinctly and systematically less than, VAS ratings of pain-sensation intensity, it was clear that subjects responded quite differently to these two pain dimensions. Affective judgements were not additionally influenced by thermal probe separation and hence by the ability to perceive stimulus size or number of thermal probes activated. 6. The results indicate that powerful spatial-summation mechanisms exist for heat-induced pain. Spatial summation of pain is likely to be subserved both by local integration mechanisms at the level of single spinothalamic-tract neurons and by recruitment of central nociceptive neurons, because spatial summation of pain occurred to approximately equal extents under conditions of thermode separations over a distance of at least 20 cm.

Adult↗

PubMed1987

Spatial frequency discrimination for sinewave gratings with random, bandpass frequency modulation: evidence for averaging in spatial acuity.

Spatial frequency difference thresholds for vertical, high contrast sinewave gratings were estimated at 1.25, 2.5, 5.0 and 10.0 cyc deg-1. Within an experiment two independent manipulations of the stimulus were employed: (1) the number of cycles of the sinewave grating was varied over a range of 2.0 to 15.0 cycles; and (2) a stationary, random frequency modulation was imposed on the sinewave. The probability density function of the frequency modulation was a Gaussian whose dispersion coefficient was varied, in different experiments, in the range of 0 to 10% of the frequency of the parent sinewave. Both of these experimental variables were found to affect the precision with which spatial frequency discrimination could be performed. The Weber fraction increased both as the number of cycles present was decreased and as the dispersion coefficient of the modulating function was increased. These two effects were independent. The data support previous psychophysical findings that spatial frequency discrimination involves averaging over the total area of the stimulus and are compatible with spatial primitive models of spatial contrast vision. The data are not compatible with those of Hirsch and Hylton (J. opt. Soc. Am. 72, 1367-1374) which suggest that spatial interval discrimination occurs solely by operation of foveal mechanisms.

Adult↗

PubMed1991

Two-dimensional spatial and spatial-frequency selectivity of motion-sensitive mechanisms in human vision.

Thresholds for detecting the direction of motion of drifting (8-Hz) vertical gratings [of spatial frequencies 0.1, 1.0, and 10.0 cycles per degree (c/deg)] were measured in the presence of masks that varied in both spatial frequency and orientation. Masks with different temporal properties were used. The specificity of masking was also measured for a stationary test grating of spatial frequency 3.0 c/deg. After suitable scaling and transformation, the masking data gave an estimate of the two-dimensional spatial-frequency tuning surface of cortical detector units in human vision. With the assumption of small-signal linearity and zero phase, the tuning surfaces were inverse Fourier transformed to give an indication of the size and structure of the psychophysical receptive fields of detector units. The results obtained with drifting test gratings and jittering (random phase) mask gratings indicate that motion-detector receptive fields increase in size (in cycles) with increasing spatial frequency but, at all spatial scales, have a length-width ratio of 1. These results are in close agreement with the summation results reported in J. Opt. Soc. Am. A 8, 1330 (1991). Using the same jittering mask stimuli and stationary test gratings, we confirm reports by Daugman [Vision Res. 24, 891 (1984)] and Harvey and Doan [J. Opt. Soc. Am. A 7, 116 (1990)] that motion-independent units have elongated receptive fields with a length-width ratio near 1.8. We conclude that the receptive fields of motion-dependent and -independent mechanisms in human vision are fundamentally different. The possibility that the orientation selectivity of a motion unit is sharpened by its selectivity for direction of motion is discussed.

Contrast Sensitivity↗

PubMed1990

Spatial-filter selection in large-scale spatial-interval discrimination.

Spatial-interval discrimination thresholds were measured for a pair of bars in the presence of other parallel bars placed far enough from the targets as to be outside the range of neural and optical blurring. Thresholds were elevated when the targets were embedded in an array of four parallel bars (two between and two flanking the targets), but not when there were only two parallels, whether the parallels were between the target bars or flanking them. The threshold elevation was larger with a 100-msec than with a 500-msec exposure duration. Attenuating the high spatial frequencies magnified the threshold elevation. The data indicate that the process responsible for spatial-interval discrimination automatically selects which spatial filters to use; it does not have to scan through all ranges of spatial filters.

Contrast Sensitivity↗

PubMed1990

The role of the amygdala and the hippocampus in working memory for spatial and non-spatial information.

Male rats received either electrolytic or sham lesions bilaterally into the amygdala, hippocampus or amygdala plus hippocampus, or were assigned to an unoperated control group. After the postoperative recovery period all lesioned and control animals were tested for the ability to master a spatial delayed non-matching-to-sample (DNMS), a visual DNMS and a visuo-tactile DNMS. Retention of these paradigms was evaluated 24 h after the last respective training session. Bilateral lesions of the amygdala severely disrupted the acquisition and retention of a DNMS paradigm with visual and visuo-tactile cues as discriminative stimuli and had no effect on the acquisition and retention of a spatial DNMS. On the contrary, bilateral lesions of the hippocampus impaired the acquisition and retention of spatial DNMS, but the animals with these lesions showed an acquisition and retention of the visual and visuo-tactile DNMS paradigms significantly better than those of animals with amygdala lesions. Combined lesions of the amygdala and hippocampus severely disrupted the acquisition and retention of the 3 paradigms. The contribution of the amygdala and the hippocampus in the working memory for spatial and non-spatial information is discussed.

Amygdala↗

PubMed1985

The development of spatial and class relations in four young children with right-cerebral-hemisphere damage: evidence for an early spatial constructive deficit.

This study followed the development of four children with right-hemisphere injury on a series of manipulative classification tasks to determine whether and how early brain injury affects the development of spatial and class relations. The children were first tested at about 2 years of age. Their data were compared with previously collected data from 18- to 42-month-old normal children, and with data from four young children with left-hemisphere injury. The results showed the children with right-hemisphere injury do not generate a particular spatial relation (next to) in their spatial groupings with the same frequency as normal or left-hemisphere damaged children, although they do generate in and on relations with normal frequency. An apparent deficit in the development of class relations is shown to be secondary to the spatial deficit, in that it is evident only in tasks that require spatial grouping.

Brain↗

PubMed1992

A new one-trial test for neurobiological studies of memory in rats. III. Spatial vs. non-spatial working memory.

Rats were submitted to object and spatial recognition tests (both based on the same paradigm) and to the radial-arm maze. The results are as follows: (1) rats could discriminate between a new and a familiar object when the retention delay was 1 min, 15 min or 60 min but not 24 h. The relationship between the level of discrimination and intertrial delays is quadratic with a maximum for 15 min. (2) Exposure to distractive stimuli during the retention delay may impair object recognition. (3) Rats discriminated between a new and a familiar space. (4) There is no correlation between the three tests which argues for a multiple form of working memory, especially a spatial and a non-spatial one. (5) Medial septal lesion did not impair object and spatial recognition memory, but the level of discrimination in the spatial recognition test was significantly reduced compared to that of control.

Aging↗

PubMed1988

The relationship of undershooting (anticipation) error in space localization to spatial dimension and spatial category width.

In this study I explored whether the degree of anticipation/habituation (undershooting/overshooting) varies with the dimension to be localized, when the method of adjustment is used in space localization. In this study, undershooting occurred for both the vertical (Group 1) and the horizontal (Group 2) dimensions, but was significant only for verticality. The magnitude of undershooting observed for verticality was significantly greater than that for horizontality. A secondary issue regarding the possible relationship between spatial category width and undershooting/overshooting was examined. It was hypothesized that greater degree of spatial category width would be associated with greater undershooting. The opposite was found: Spatial category width was negatively related to undershooting. Finally, within each group, very high consistency of magnitude of spatial category width was observed (rs greater than .90), despite the fact that spatial category width showed shrinkage over the course of the study.

Cognition↗

PubMed2026

ARCADIA reveals spatially dependent transcriptional programs through integration of scRNA-seq and spatial proteomics.

MOTIVATION: Cellular states are strongly influenced by spatial context, but single-cell RNA sequencing (scRNA-seq) loses information about local tissue organization, while spatial proteomic assays capture limited marker panels that constrain transcriptomic inference. Integrating these modalities can elucidate how spatial niches shape transcriptional programs, yet existing approaches depend on either feature-level correspondence such as gene-protein linkage or cell-level barcode pairing, which is often unavailable. RESULTS: We present ARCADIA (ARchetype-based Clustering and Alignment with Dual Integrative Autoencoders), a generative framework for cross-modal integration that operates without cell barcode pairing and does not assume direct feature-to-feature correspondence. ARCADIA identifies modality-specific archetypes, that is, convex combinations of cells representing extreme phenotypic states, and aligns these anchors across modalities by minimizing the discrepancy between their cell-type composition profiles. The aligned archetypes define a shared coordinate system that anchors dual variational autoencoders (VAEs) trained with cross-modal geometric regularization, preserving archetype structure and spatial neighborhood information while enabling bidirectional translation between modalities. On semi-synthetic CITE-seq data, ARCADIA outperforms existing weak-linkage methods. Applied to independent human tonsil scRNA-seq and CODEX data, ARCADIA reconstructs known tissue architecture and reveals spatially dependent transcriptional programs linking B-cell maturation and T-cell activation or exhaustion to microenvironmental niches. AVAILABILITY AND IMPLEMENTATION: Source code is accessible at https://github.com/azizilab/ARCADIA_public. Reproducibility scripts and data are available at https://github.com/azizilab/arcadia_reproducibility.

Proteomics↗

PubMed1982

Three-dimensional spatial, density, and temporal resolution of the dynamic spatial reconstructor.

Spatial, density, and temporal resolution of the dynamic spatial reconstructor (DSR), a multiple X-ray source, high speed, computed tomography scanning system, are evaluated. Hole-pair resolution was evaluated in a stationary phantom surrounded with air, 15 cm of water, or 20 cm of water. Temporal resolution was evaluated by rotation of one of the resolution phantoms during the scan, and with a balloon inflated to a known volume and at a known rate to approximate a typical left ventricular chamber volume and filling rate. These studies confirmed that the spatial resolution is essentially the same in the transverse and axial directions, and that retrospective manipulation of the image data is important for maximization of spatial and density resolution in any structure under examination by obtaining a tradeoff with partial-volume and motion-blurring effects. Maximum spatial resolution in the scanned volume was shown, under ideal conditions, to be greater than five hole pairs per centimeter. Under conditions of intravenous injection of contrast agent, the resolution of blood vessels in an experimental animal approximately 25 kg in weight is expected to be on the order of three hole pairs per centimeter; and in an adult human weighting approximately 60 kg, a resolution of about two hole pairs per centimeter is to be expected.

Angiography↗

PubMed1983

Spatial-frequency adaptation affects spatial-probability summation.

The effects of spatial-frequency adaptation on spatial-probability summation were investigated by two techniques: the measurement of the dependence of cosine grating sensitivity on the number of cycles presented and the determination of the frequency-of-seeing curve for a cosine grating. Both measurements indicate that the contribution of spatial-probability summation to adapted grating thresholds is reduced in comparison with unadapted conditions. This reduction in the effects of spatial-probability summation, together with the decrease in local sensitivity, which depends on the spatial inhomogeneity of the visual system, is sufficient to account for the threshold elevation aftereffect measured when adapting and testing with cosine gratings.

Adaptation, Ocular↗