Fixation on Histology

Spatial Omics: A Molecular Glimpse into the Complex World of Histotechnology


In the ever-evolving landscape of molecular biology and histotechnology, a paradigm shift is underway - the rise of spatial omics. This revolutionary approach has ushered in a new era of exploration, offering insights that were once unimaginable. In this academic discussion, we will delve into the intriguing realm of spatial omics, exploring its significance, methodologies, and potential applications in histotechnology.

Unveiling the Spatial Omics Landscape

The molecular world is complex, dynamic, and exquisitely organized. To truly understand it, we need more than just a broad overview of molecular components; we need to uncover where each component is situated. This is where spatial omics comes into play, bridging the gap between traditional molecular analysis and spatial context.

The Significance of Spatial Omics

Unmasking Hidden Insights

One of the key advantages of spatial omics is its ability to reveal hidden insights within complex tissues. By providing a spatial dimension to molecular data, it enables researchers to pinpoint the exact location of specific molecules, genes, or proteins within a tissue sample. This newfound level of precision brings molecular biology to a new level of granularity.

Revealing Tissue Heterogeneity

In the realm of histotechnology, the significance of spatial omics is amplified by its ability to unravel tissue heterogeneity. Histological samples are inherently diverse, containing a variety of cell types, each contributing differently to the tissue's overall function. Spatial omics allows for the differentiation of these cell types, providing a comprehensive understanding of the tissue's intricate architecture.

Applications in Disease Research

For disease research, the implications of spatial omics are profound. Researchers can now explore the molecular changes associated with specific diseases in the context of the affected tissues. By pinpointing the exact locations of disease markers or altered genes, spatial omics helps in developing a deeper understanding of diseases, potentially leading to more targeted treatments.

Methodologies of Spatial Omics

Imaging Mass Cytometry (IMC)

One of the primary methodologies within spatial omics is Imaging Mass Cytometry (IMC). IMC combines the power of mass spectrometry and microscopy to simultaneously detect multiple proteins within a tissue sample. By using metal-tagged antibodies, IMC provides high-resolution images of the spatial distribution of proteins. This technology has been instrumental in studying protein interactions, immune responses, and tumor microenvironments.

Spatial Transcriptomics

Spatial transcriptomics is another key methodology, providing insights into the spatial distribution of gene expression. Techniques like in situ hybridization and RNA-sequencing are employed to analyze the spatial organization of RNA molecules within a tissue sample. This approach allows researchers to visualize which genes are active in specific regions, shedding light on cellular function and regulatory pathways.

Single-Cell RNA Sequencing (scRNA-seq)

Single-Cell RNA Sequencing, although not traditionally considered a spatial omics technique, can be integrated into spatial omics analyses. By examining the gene expression profiles of individual cells within a tissue, scRNA-seq data can be overlaid onto histological images to provide spatial context. This approach has proven invaluable in understanding cellular heterogeneity and interactions within tissues.

Applications and Future Directions


Spatial omics has made substantial contributions to neuroscience by elucidating the molecular intricacies of the brain. Researchers have been able to map the expression of specific genes within different brain regions, shedding light on neural circuits and disorders like Alzheimer's and Parkinson's disease. The potential for further breakthroughs in understanding brain function is vast.

Cancer Research

In oncology, spatial omics is becoming a powerful tool for characterizing the tumor microenvironment. By mapping the spatial distribution of immune cells, cancer cells, and stromal components, researchers gain a comprehensive view of the interactions that drive tumorigenesis and treatment resistance. This has the potential to reshape cancer therapy and prognosis.

Regenerative Medicine

Regenerative medicine stands to benefit from spatial omics by providing insights into tissue regeneration and development. By understanding the molecular cues guiding tissue repair and growth, scientists can enhance the design of regenerative therapies and accelerate their translation into clinical applications.

Challenges and Future Prospects

While spatial omics holds immense promise, it also presents challenges. The integration of diverse data modalities, computational analysis, and the standardization of protocols are among the hurdles researchers must address. Additionally, there is a need for continued innovation in spatial omics technologies to enhance their accessibility and affordability.


Spatial omics is a groundbreaking approach that is reshaping the field of histotechnology. It brings the molecular world into focus, providing a spatial dimension to our understanding of complex tissues. With applications ranging from neuroscience to oncology and regenerative medicine, spatial omics offers unprecedented insights and has the potential to revolutionize disease research and treatment.

In the pursuit of comprehending the molecular intricacies of histological samples, spatial omics is a powerful ally. As technology continues to evolve and research in this field progresses, we can anticipate remarkable discoveries and the realization of its full potential.

Histology for Spatial Omics Special Collection Series

The NSH Journal of Histotechnology is creating a Histology for Spatial Omics Special Collection Series.  Preparing high-quality samples or tissue sections for spatial omics analysis is the first gatekeeper to a successful discovery. Many pre-analytic factors such as sample collection, preservation, embedding, mounted section storage and handling, and analytic factors such as fixation, staining, and detection reagents application, affect not only the spatial omics assay efficacy but also the accuracy of the data interpretation. In this ongoing special edition series, JOH would like to collect commentaries, perspectives, reviews, guidelines, research articles, technical notes, protocols, and case studies on any aspect of spatial omics technology and research. Learn More




12-06-2023 12:11

Thank you for creating a clear picture of how all these assays and tests compliment each other.  I am looking forward to hearing/reading more about this.

12-01-2023 11:35

Looking forward to the Spatial Omics collections series from the JOH!