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TOPICAL COLLECTIONS

Spatial Biology Uncovered: Cutting-Edge Techniques and Practical Applications
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Guest Editors

Ankit Agrawal

Ankit Agrawal

Department of Computational Biology of Spatial Biomedical Systems Würzburg Institute of Systems Immunology, Würzburg, Germany

<p><span style="color: rgb(0, 0, 0);">Dr. Ankit Agrawal obtained his Ph.D. in Computational Biology from HBNI, Mumbai, India, in 2019. During his doctoral research, he developed biophysical models of chromatin architecture, spanning scales from motifs to individual chromosomes. Dr. Agrawal conducted a brief postdoc in the developmental biology laboratory of Elazar Zelzer at the Weizmann Institute of Science, Israel, from 2018-2020, where he developed a computational pipeline to define cell state based on morphological features. This led to the discovery that morphological cell states delineate principal axes in bone tissue variability. His research demonstrated that spatiotemporal clusters of these morphological cell states are responsible for different bone growth strategies in adult and embryonic mice. Since 2021, Dr. Agrawal has been working in the lab of Dominic Grün, where he developed NiCo, a computational tool for identifying cell state covariation in the colocalized neighborhood by integrating spatial transcriptomics and single-cell RNA sequencing data. Dr. Agrawal's research interest focuses on understanding cellular states and cell state transitions in healthy and diseased tissues.&nbsp;</span></p>

Madhumala K. Sadanandappa

Madhumala K. Sadanandappa

Department of Pathology and Laboratory Medicine, Dartmouth Hitchcock Medical Center

<p>Dr. Madhumala K. Sadanandappa earned her PhD from the National Center for Biological Sciences, Bangalore, followed by a Human Frontier Science Program postdoctoral fellowship at the Geisel School of Medicine, Dartmouth College, USA. Using animal models of human disease in her research, she uncovered circuit, cellular, and molecular mechanisms underlying behavioral habituation, olfactory learning and memory, host-parasitoid interactions, and the function of conserved disease-causing genes.</p><p><br></p><p>Dr. Sadanandappa leads spatial biology initiatives at Dartmouth Hitchcock Medical Center. As part of the Emerging Diagnostics and Innovative Technologies Program, she oversees the validation of assays and the development of data analysis pipelines for high-plex proteomics, transcriptomics, and multi-omics<span style="color: rgb(28, 28, 28);">.</span> Her research focuses on deciphering tumor microenvironment interactions to identify biomarkers for diagnosis and therapeutics.</p>

Collection Overview

Spatial biology is transforming our ability to study cellular processes within their native tissue environments by integrating spatial proteomics, transcriptomics, metabolomics, genomics, and epigenomics. This powerful approach provides high-resolution insights into cell-cell communication, tissue organization, disease mechanisms, and therapeutic strategies. The advancement of this field depends on robust experimental techniques, innovative methodologies, and optimized workflows.

This method collection invites researchers, clinicians, and industry professionals to showcase state-of-the-art techniques, workflows, and instrumentation that drive spatial biology forward in academic research, biotechnology, and industry. 

We welcome contributions on the following:

  • High-resolution spatial omics techniques – Imaging, molecular profiling, single-cell analysis, high-plex, and multi-omics approaches
  • Optimized protocols and experimental workflows – Protocol development, automation, and high-throughput adaptations
  • Instrumentation and data acquisition – Advances in imaging, sequencing, integrating with H&E, multiplexing, and assay standardization
  • Computational approaches – Data analysis tools, multi-omics integration, and visualization tools
  • Disease and therapeutic applications – Spatial biology in disease modeling, biomarker discovery, therapeutic targets, and precision medicine

We encourage original research methodologies, technical reports, and case studies on experimental design, protocol optimization, and computational solutions for spatial biology challenges.

Join us in advancing spatial biology by contributing cutting-edge research!

Articles

Multi-Modal Spatial Metabolomics with Mid-Infrared Microscope Guided Mass Spectrometry Imaging

Multi-Modal Spatial Metabolomics with Mid-Infrared Microscope Guided Mass Spectrometry Imaging

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Cited by 2

2025

Mining Spatial Transcriptomics Datasets using DeepSpaceDB
10:16

Abstracts

Intravital Microscopy-Guided Live-Cell Isolation from Intact Tissue to Link Dynamics of Leukemia Progression with Single-Cell Transcriptional Programs

Christa Haase*1

1Departments of Bioengineering and Physics, Northeastern University