Shamini Ayyadhury, PhD

Postdoctoral Fellow (University of Toronto, Princess Margaret Cancer Research Center)

Director, Panoramics – A Vision

Computational scaling

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Learning Objectives

• By the end of this lecture, you will:

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• Review the 2um and 16um unbinned and binned images
• Appreciate what the different bins mean
• Appreciate the difference between scale and bin size
• Compare the resolution, scale and information content between single molecule , spot based
• Develop an intuition on when to go subcellular and when to increase bin size.

Why is scale important?

Single-molecule localization microscopy, Nature Reviews Methods Primers volume 1, Article number: 39 (2021)

Imaging-based systems

https://www.10xgenomics.com/support/software/xenium-panel-designer/latest/tutorials/xenium-panel-design-concepts-terms

Imaging-based systems

https://www.10xgenomics.com/support/software/space-ranger/latest/getting-started/space-ranger-glossary

Sequencing-based systems

https://stereopy.readthedocs.io/en/v1.4.0/Tutorials/CellBin_Clustering.html

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

What is scale?

Here we define scale as the ability to look at spots and the resolution is defined by the point-to-point distances

Stereo-seq

VisiumHD

https://stereopy.readthedocs.io/en/v1.4.0/Tutorials/CellBin_Clustering.html

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

What is scale?

Here we define scale as the ability to look at single cells

Stereo-seq

VisiumHD

What is scale?

Here we define scale as the ability to look at single molecular localization points

Ayyadhury, S, Unpublished data

Mouse xenograft model (humanGBM)

Coloured by blood vessels, tumor cells and immune cells

Coloured by cell-types

Ayyadhury, S, Unpublished data

What is scale?

Here we define scale as the ability to look at single molecular localization points

Human GBM tissue source – Dirks lab

Xenium

Why is scale important? And which resolution will help me answer these questions?

Conclusion

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Scale matters. It is not just about bins. It is the bandwidth over which you extract ‘information that is relevant, meaningful’.

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You will review a very simple script later. But the aim of the script is if a bin or scale size is not giving you ‘above noise’ information, then rethink your concept of scale.

Contact information :

Shamini Ayyadhury

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

Panoramics – A Vision : shamini.ayyadhury@panoramics-a-vision.com

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