• What is spatial?
• Knowing the spatial diaspora – an overview of current technologies/platforms
• What’s fad, fiction and reality?
• Understanding platform potential, limitations and open access capacity
• Computational diversity, development and introspective growth
• Appreciating wet lab & engineering expertise, technical advancement, innovation and skills
• What this workshop will teach you and your approach to this course.

Panorama of Spatial Biology

• What is spatial?
• Knowing the spatial diaspora – an overview of current technologies/platforms
• What’s fad, fiction and reality?
• Understanding platform potential, limitations and open access capacity
• Computational diversity, development and introspective growth
• Appreciating wet lab & engineering expertise, technical advancement, innovation and skills
• What this workshop will teach you and your approach to this course.

Panorama of Spatial Biology

• What is spatial?

• Is it single cell?

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• Is it only protein and gene expression?

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• Is it cell-cell communication?

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• Better than bulk or single cell feature extraction?

• What is spatial?

• Is it single cell?

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• Is it only protein and gene expression?

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• Is it cell-cell communication?

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• Better than bulk or single cell feature extraction?

• It is not single cell (only) – it is the study of collective relationships by taking into account snapshot neighborhood relationships

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• It may or may not be molecular in nature

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• CC is just one task within the broader array of tasks that we can apply over spatial

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• It gives a different vantage point to investigate and learn

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• What is spatial?
• Knowing the spatial diaspora – an overview of current technologies/platforms
• What’s fad, fiction and reality?
• Understanding platform potential, limitations and open access capacity
• Computational diversity, development and introspective growth
• Appreciating wet lab & engineering expertise, technical advancement, innovation and skills
• What this workshop will teach you and your approach to this course.

Panorama of Spatial Biology

• Knowing the spatial diaspora – an overview of current technologies/platforms
• What’s fad, fiction and reality?

Spatiotemporal omics for biology and medicine , Cell, Volume 187, Issue 17, 22 August 2024, Pages 4488-4519

For the purposes of today’s objectives – focus on transcriptomics

1. Capture the molecules that govern the Central Dogma
2. Two broad engineering principles
• Sequencing-based
• Imaging-based

• Knowing the spatial diaspora – an overview of current technologies/platforms
• What’s fad, fiction and reality?

CurioSeeker

Slide-tags enables single-nucleus barcoding for multimodal spatial genomics, Nature volume 625, pages101–109 (2024)

VisiumHD

Stereo-seq

https://www.10xgenomics.com/

Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays, Cell 185, 1777–1792

• Knowing the spatial diaspora – an overview of current technologies/platforms
• What’s fad, fiction and reality?

Xenium

Merscope

CosMX Image taken from https://nanostring.com/products/cosmx-spatial-molecular-imager/single-cell-imaging-overview/

Image taken from : http://www.sagecreation.com.cn/en/product/detail/?cid=2256

Image taken from - https://images.app.goo.gl/BnUCDBNsKwYr8RtM7

Willis, A, 2025, Single cell approaches define neural stem cell niches and identify microglial ligands that can enhance precursor-mediated oligodendrogenesis, Cell Reports 44, 115194

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• Knowing the spatial diaspora – an overview of current technologies/platforms
• What’s fad, fiction and reality?

Pixel-seq

Singular Genomics

https://www.uwgulab.org/research/projects/pixel-seq

https://singulargenomics.com/

Pre-commercial

• Knowing the spatial diaspora – an overview of current technologies/platforms
• What’s fad, fiction and reality?

Pixel-seq

Singular Genomics

Stellaromics – 3D

https://www.uwgulab.org/research/projects/pixel-seq

https://singulargenomics.com/

https://stellaromics.com/

Three-dimensional intact-tissue sequencing of single-cell transcriptional states, Science. 2018 July 27; 361(6400)

Pre-commercial

• Knowing the spatial diaspora – an overview of current technologies/platforms
• What’s fad, fiction and reality?

Pixel-seq

Singular Genomics

Stellaromics – 3D

https://www.uwgulab.org/research/projects/pixel-seq

https://singulargenomics.com/

https://stellaromics.com/

Three-dimensional intact-tissue sequencing of single-cell transcriptional states, Science. 2018 July 27; 361(6400)

I have not covered every spatial transcriptomics platform

This lecture excludes other spatial modalities (i.e MSI, Protein, epigenomics , temporal spatial patterning etc)

• Sometimes the platforms are similar – same design – same underlying principles – low diversity
• Sometimes, the underlying principles are similar but chemistry and engineering differences can contribute to differences in what we detect
• Understand how your technology works so that it does not become fad.

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• Maximize the potential
• Think hard about older techniques

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• Knowing the spatial diaspora – an overview of current technologies/platforms
• What’s fad, fiction and reality?

• What is spatial?
• Knowing the spatial diaspora – an overview of current technologies/platforms
• What’s fad, fiction and reality?
• Understanding platform potential, limitations and open access capacity
• Computational diversity, development and introspective growth
• Appreciating wet lab & engineering expertise, technical advancement, innovation and skills
• What this workshop will teach you and your approach to this course.

Panorama of Spatial Biology

• Understanding platform potential, limitations and open access capacity

What is platform potential?

• Some platforms have creative concepts
• Some have good engineering structure
• Some have robust chemistry
• Some have high sensitivity
• Some have good specificity
• Some have good PR team
• Some have convenient / user-friendly packages
• Some of a more reproducible wet-lab processing
• Some are computationally more tractable

• Understanding platform potential, limitations and open access capacity

What is platform potential?

• Some platforms have creative concepts
• Some have good engineering structure
• Some have robust chemistry
• Some have high sensitivity
• Some have good specificity
• Some have good PR team
• Some have convenient / user-friendly packages
• Some of a more reproducible wet-lab processing
• Some are computationally more tractable

To understand the science

• What is spatial?
• Knowing the spatial diaspora – an overview of current technologies/platforms
• What’s fad, fiction and reality?
• Understanding platform potential, limitations and open access capacity
• Computational diversity, development and introspective growth
• Appreciating wet lab & engineering expertise, technical advancement, innovation and skills
• What this workshop will teach you and your approach to this course.

Panorama of Spatial Biology

• Computational diversity, development and introspective growth

Since you are all here to learn the basics of experimental and computational processing

Standard processing – for quick but effective analysis

These are very good for absolute beginners

1. Seurat
• https://satijalab.org/seurat/articles/visiumhd_analysis_vignette

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• Scanpy
• https://scanpy-tutorials.readthedocs.io/en/multiomics/analysis-visualization-spatial.html
• https://github.com/scverse/spatialdata-io

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Wonderful tools, little advanced but great spatial and scale tools

1. GiottoSuite
• https://drieslab.github.io/Giotto_website/articles/VisiumHD_Human_Colorectal_Cancer.html

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These are not limited to only visiumHD

• Computational diversity, development and introspective growth

Since you are all here to learn the basics of experimental and computational processing

Advanced computational analysis?

Many methods are still under development

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Method development depends on your platform and biological question

1. Subcellular resolution
• 2um (VisiumHD), 250nm (stereo-seq), 10nm(Slide-tag)
• Sensitivity (2um, 8um, 16um) > label transfer, integration, transformation methods
• Algorithmic decoding (Single molecule imaging-based i.e Xenium, StarMap etc)
2. Definition of simplest unit
• Spot versus ‘single-cell’ – type of QC, extent of pre-processing, deconvolution)

• Computational diversity, development and introspective growth

Since you are all here to learn the basics of experimental and computational processing

Advanced computational analysis?

Many methods are still under development

​

Method development depends on your platform and biological question

1. Subcellular resolution
• 2um (VisiumHD), 250nm (stereo-seq), 10nm(Slide-tag)
• Sensitivity (2um, 8um, 16um) > label transfer, integration, transformation methods
• Algorithmic decoding (Single molecule imaging-based i.e Xenium, StarMap etc)
2. Definition of simplest unit
• Spot versus ‘single-cell’ – type of QC, extent of pre-processing, deconvolution)

Biological Question

• Computational diversity, development and introspective growth

Since you are all here to learn the basics of experimental and computational processing

Advanced computational analysis?

https://www.10xgenomics.com/analysis-guides/segmentation-visium-hd

Segmentation

Problem is the same

But the solution and algorithmic approach will be different

• What is spatial?
• Knowing the spatial diaspora – an overview of current technologies/platforms
• What’s fad, fiction and reality?
• Understanding platform potential, limitations and open access capacity
• Computational diversity, development and introspective growth
• Appreciating wet lab & engineering expertise, technical advancement, innovation and skills
• What this workshop will teach you and your approach to this course.

Panorama of Spatial Biology

• Appreciating wet lab & engineering expertise, technical advancement, innovation and skills

Since you are all here to learn the basics of experimental and computational processing

Wet lab methodologies, engineering and chemistry guide the merits of a system

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1. A tremendous amount of time, effort, creativity and intellect goes into development.
2. The worth of computational analysis is as good as the input we provide
3. Post-computational analysis guides wet-lab developments

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Two way process

Since you are all here to learn the basics of experimental and computational processing

Highly recommend to read this paper’s MATERIALS AND METHODS

Formation of Cartana AB (Swedish company)

ISS technology that was later integrated into 10xGenomics Xenium

• Appreciating wet lab & engineering expertise, technical advancement, innovation and skills

Since you are all here to learn the basics of experimental and computational processing

Highly recommend to read this paper’s MATERIALS AND METHODS

Formation of Cartana AB (Swedish company)

ISS technology that was later integrated into 10xGenomics Xenium

Cell culture and sample preparation.

�Tissue sections.

�In situ reverse transcription.

�Gap-fill padlock probing.

�Barcode padlock probing.

�RCA and RCA products detection.

�Sequencing by ligation.

�Image acquisition and analysis.

These are the MM headers

• Appreciating wet lab & engineering expertise, technical advancement, innovation and skills

Since you are all here to learn the basics of experimental and computational processing

Highly recommend to read this paper’s MATERIALS AND METHODS

Formation of Cartana AB (Swedish company)

ISS technology that was later integrated into 10xGenomics Xenium

Cell culture and sample preparation.

�Tissue sections.

�In situ reverse transcription.

�Gap-fill padlock probing.

�Barcode padlock probing.

�RCA and RCA products detection.

�Sequencing by ligation.

�Image acquisition and analysis.

These are the MM headers

Take your garbage-in, garbage-out seriously

• Appreciating wet lab & engineering expertise, technical advancement, innovation and skills

Since you are all here to learn the basics of experimental and computational processing

Highly recommend to read this paper’s MATERIALS AND METHODS

Formation of Cartana AB (Swedish company)

ISS technology that was later integrated into 10xGenomics Xenium

Cell culture and sample preparation.

�Tissue sections.

�In situ reverse transcription.

�Gap-fill padlock probing.

�Barcode padlock probing.

�RCA and RCA products detection.

�Sequencing by ligation.

�Image acquisition and analysis.

These are the MM headers

And this is how we advance forward, when we learn from each other

• Appreciating wet lab & engineering expertise, technical advancement, innovation and skills

• What is spatial?
• Knowing the spatial diaspora – an overview of current technologies/platforms
• What’s fad, fiction and reality?
• Understanding platform potential, limitations and open access capacity
• Computational diversity, development and introspective growth
• Appreciating wet lab & engineering expertise, technical advancement, innovation and skills
• What this workshop will teach you and your approach to this course.

Panorama of Spatial Biology

• What this workshop will teach you and your approach to this course.

• This workshop is more computational heavy
• Module 1 – wet lab – steps to have hands on is administratively not feasible
• Modules 2-6 computational
• Computational practical is foundational
• Limited computational bandwidth (bulk > single cell > spatial > spatial with varying resolutions)
• Balance for the mixture of our participant cohort
• VisiumHD – spot based, 10xGenomics

• However, this workshop is meant to also encourage participants to think critically about how to use or analyze this platform
• Many of the concepts that we teach IS APPLICABLE to other spatial platforms (including other spatial non-transcriptomic modalities)
• Even if at times the analysis may not be as challenging, there will be discussion points and participation and innovative brain-storming is encouraged

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• It is not the brand – it is the ideas , skills on how you approach spatial problems that will be the take-home points from this workshop.

The world is your oyster

Plant & insect

Medical applications

VR & AR

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Conclude this talk and welcome everyone to ISO2025vHD

Thank co-organizers (Nia Hughes (bioinformatics.ca), Urja Verma (BSCI)

Instructors/TAs : Savannah Kilpatrick, Alyona Ivanova, Amina Abow, Melanie Peralta, Joan Kant, Yiyan Wu,

Jawairia Atif, Dina Karamboukas

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Contact information :

Shamini Ayyadhury

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Academic brainstorming & consultation : shamini.ayyadhury@utoronto.ca

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Panoramics – A Vision

Panoramics – A Vision :

General enquiries : panoramics@panoramics-a-vision.com�

Connect with me

Panoramics

Upcoming single-cell and spatial programs that will be updated in the coming weeks & months

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”inspire”, “enlighten”, “challenge” – me chapters

We are on a Coffee Break & Networking Session

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