Spatial transcriptomics

Analyze gene expression within tissue using imaging-based and sequencing-based spatial transcriptomics. Guided R/Bioconductor labs cover cell segmentation, quality control, interactive exploration and integration with single-cell datasets. Downstream analyses characterize cellular niches, neighbourhoods and cell–cell communication. The course concludes with project design and a team hackathon using participant or public data, connecting computational outputs to biological interpretation. 2026-12-14–2026-12-18, 14:00–18:00 daily, Europe/Berlin (CET, UTC+01:00). Online course; fee €530. Designe

Explore gene expression while preserving the spatial context lost in bulk and conventional single-cell sequencing. This workshop compares imaging-based and sequencing-based spatial transcriptomics and works through public human and mouse datasets. Hands-on analysis covers loading, quality control, segmentation, integration, cell typing and identification of cellular neighborhoods and niches. Intended for biomedical and life-science graduates or postgraduates with some R experience; demonstrations use R and Python code is also supplied. Familiarity with RNA sequencing is helpful. Sessions on 1

This practical course introduces spatial-omics methods, particularly multiplex immunofluorescence and spatial transcriptomics, and helps researchers choose suitable approaches for their questions. Hands-on sessions teach open-source imaging methods designed for cost-effective experiments. Training follows the full workflow from custom reagents and sample preparation to microscopy data acquisition, image processing and basic analysis. The intended participants are PhD students, postdocs and staff in tissue biology or biomedicine with experience in tissue handling, immunofluorescence and basic m

Analyse bulk, single-cell and spatial transcriptomics alongside chromatin, CRISPR and proteomics datasets to support oncology target discovery. The scientist will build reproducible analysis workflows, integrate evidence across experiments and collaborate with laboratory researchers on target validation. The advertised salary range is USD 142,000–171,150. Applications are available on the employer’s Greenhouse page; no fixed deadline is stated.

…and bright-field microscopy, spatial transcriptomics, anterograde tracing and diffusion MRI into a whole-brain multimodal atlas. Research topics include neuron and axon tracing in dense 3D data, generative models for synthetic tracing ground truth, images exceeding GPU memory, cross-modal image registration, biomedical foundation models, and diffusio

Map brain cell types and disease-related changes using high-throughput spatial transcriptomics on human tissue. Run MERFISH+ imaging workflows, perform quality control and primary image analysis, organize experiment metadata, maintain instruments and improve protocols in the Brain Health accelerator. The annualized salary range is USD 77,150–94,550. Work is primarily onsite at 615 Westlake Avenue North, Seattle, during weekday business hours.

…RNA and chromatin-accessibility data, spatial transcriptomics and integration across datasets. The scholarship supports postdoctoral research in Solna, connecting computational methods with molecular and cellular neuroscience. The award is intended for eligible researchers coming from outside Sweden and is tax-exempt; no amount is advertised. Scholarships are normally set for twelve months at a time, up to two years. Apply by 26 October 2026.

Neuronal networks are at the core of the brain's vast computational capacities. Different strategies have each brought deep insights into their architecture. Yet, each method is limited in its capacity to resolve even simple subnetworks of single cells, due to the current compromise between throughput, resolution, and coverage. Viral projection tracing helps establish regional connectomes of mammalian brains. In combination with additional modification, the method can reveal cell-type-specific projection patterns. However, these maps lack single-neuron resolution. Monosynaptic connectivity tra

The habenula (Hb) is a diencephalic brain region implicated in adaptive behaviors and neuropsychiatric disorders. Two main Hb subdivisions, the lateral habenula and medial habenula, have been shown to play different roles in diverse behaviors, ranging from classical and operant learning to the prediction of outcomes, fear, addiction, and social interactions. However, our understanding of cytoarchitecture and topography of the vertebrate Hb, as well as how different Hb microcircuits are organized across species, remains limited. In this study, we utilized a combination of single-cell and spatia

Advancements in spatial imaging technologies (SIT) have broadened transcriptomic discovery capacity. Yet, development of orthogonal technologies for follow-up translational studies have trailed. We have developed MSIA that utilizes non-temporal, optical barcodes by combining the advantages of RNAscope™ double-Z probes and Hiplex v2 signal amplification technology.Fresh-frozen and FFPE brain coronal sections were collected from C57BL/6J mice of 3 age groups: 1 month, 6 months, and 12 months, respectively. MSIA was executed in 3 cycles, with 100 RNA targets in cycles 1&2 and then up to 4 pro

…To address this, we have used spatial transcriptomics and single-nucleus RNA sequencing to characterize the molecular events in mouse models of prodromal PD. We have used two different PD models: a) a progressive dopamine degeneration model of mitochondrial dysfunction (MitoPark mice), and b) a mild toxin model based on a low-dose unilateral 6-hydr

The function of the cerebral cortex relies on the cellular balance between excitatory (pyramidal cells) and inhibitory neurons (interneurons), which is disrupted in disorders such as autism or schizophrenia. The emergence of cortical function during postnatal development relies on spontaneous synchronous activity among large groups of pyramidal cells and interneurons, which later desynchronise for efficient information processing. Before this network activity shift, interneuron numbers are adjusted through activity-dependent programmed cell death mechanisms. However, the extent to which the ad

Understanding the striatal neuronal diversity is key to decipher the basal ganglia circuit and to untangle the complex neurological and psychiatric diseases affecting this brain structure. Two main neuronal groups are found in the dorsal striatum: the abundant medium size projecting neurons (MSNs) and the local neurons or interneurons. While recent studies in the mouse striatum employing advanced technologies have unveiled a significantly broader spectrum of neuronal subtypes, it remains unclear how this diversity extends to the human brain. Here, we conducted single nuclei RNA-seq (snRNA-seq)

Parkinson’s disease (PD) is characterized by the selective loss of dopaminergic neurons in the Substantia Nigra and Lewy body formation, resulting in a progressive neurodegenerative disorder with movement defects. The impairment of dopaminergic innervation in PD hinders the two main projection systems from the dorsal striatum (Putamen, Pu, and Caudate Nucleus, CN) from effectively responding to cortical and thalamic signals.A potential role of Oligodendrocytes (OLs) in PD was pointed out by recent works describing GWAS PD variants associated with OLs (Bryois et al, Nat Genet, 2020), PD genes e

Neural stem cells (NSCs) in the adult mouse brain contribute to lifelong brain plasticity. NSCs in the adult ventricular-subventricular zone (V-SVZ) are heterogeneous and, depending on their location in the niche, give rise to different types of olfactory bulb interneurons. We have recently showed that pregnancy activates specific stem cell subpopulations residing in regionally-distinct domains of the niche, with different temporal dynamics. The recruitment of ‘pregnancy-associated’ NSCs is transient, and results in a temporally-controlled generation of different subtypes of olfactory bulb int

…By employing spatial transcriptomics and sin

…Single-cell RNA sequencing and spatial transcriptomics performed on both postnatal and adult mouse cerebella unveiled the transcriptome of established astrocyte

Despite decades of meticulous classification of spinal subtypes involved in central pattern generation (CPG), the synaptic architecture and mechanisms underlying locomotion remain elusive. We recently proposed a random network model, based on balanced excitation/inhibition, termed the Balanced Sequence Generator (BSG). This model recapitulated the rhythmic sequences observed in the cord and accommodated multi-functionality critical to CPGs. However, it did not include or address the diversity of spinal cell types. Here, we present a new approach that expands the BSG-framework to reconcile netw

…aims to dissect cell-type-specific and spatial transcriptomic alterations in AD, with a particular focus on a subgroup of Down Syndrome (DS) patients afflicted by AD (AD in DS). Our objective is to explore the overlaps and distinctions between sporadic AD (sAD) and AD in DS, thereby providing insights that may bridge the gap between animal models and human AD conditions. We employed spatial transcriptomics (ST) in conjunction with

…cortex of 5 newborns, using Visium Spatial Gene Expression kits, followed by high-resolution i

The precise spatial localization of molecular signals within tissues richly informs the mechanisms of tissue formation and function. Here, we’ll introduce Slide-seq, a technology which enables transcriptome-wide measurements with near-single cell spatial resolution. We’ll describe recent experimental and computational advances to enable Slide-seq in biological contexts in biological contexts where high detection sensitivity is important. More broadly, we’ll discuss the promise and challenges of spatial transcriptomics for tissue genomics. Lastly, we’ll touch upon novel molecular recording tech

…Using single-cell RNA sequencing and spatial transcriptomics we identified molecular signatures that can be used to localize and monitor distinct microglia functional states in the human and mouse brain. Our results show that microglia assume