Dharmesh D Bhuva
@bhuvad.bsky.social
Post-doctoral researcher at the University of Adelaide (South Australian Immunogenomics Cancer Institute) with an interest in cancer systems biology and spatial omics data.
Reposted by Dharmesh D Bhuva
You need to be careful with how you approach library size normalisation in spatial txomics, or what you could end up eliminating organs / meaningful structures.
-- Dharmesh Bhuva 2/
-- Dharmesh Bhuva 2/
December 3, 2024 at 1:00 AM
You need to be careful with how you approach library size normalisation in spatial txomics, or what you could end up eliminating organs / meaningful structures.
-- Dharmesh Bhuva 2/
-- Dharmesh Bhuva 2/
Reposted by Dharmesh D Bhuva
Many sources of variation in spatial -omics:
- Tissue structure / library sizes
- Images captured for each FOV (Field of View) separately
- Antibody-binding affinity differences
- Cells overlapping in z-axis
- Partial cells captured
- Background intensity
- Instrument noise
@bhuvad.bsky.social 3/
- Tissue structure / library sizes
- Images captured for each FOV (Field of View) separately
- Antibody-binding affinity differences
- Cells overlapping in z-axis
- Partial cells captured
- Background intensity
- Instrument noise
@bhuvad.bsky.social 3/
December 3, 2024 at 1:11 AM
Many sources of variation in spatial -omics:
- Tissue structure / library sizes
- Images captured for each FOV (Field of View) separately
- Antibody-binding affinity differences
- Cells overlapping in z-axis
- Partial cells captured
- Background intensity
- Instrument noise
@bhuvad.bsky.social 3/
- Tissue structure / library sizes
- Images captured for each FOV (Field of View) separately
- Antibody-binding affinity differences
- Cells overlapping in z-axis
- Partial cells captured
- Background intensity
- Instrument noise
@bhuvad.bsky.social 3/
Reposted by Dharmesh D Bhuva
Library size confounds biology in spatial transcriptomics data.
Single cell RNA-seq tools & ideologies will NOT translate to spatial molecular data!
genomebiology.biomedcentral.com/articles/10....
@bhuvad.bsky.social #multiomics2024 4/
Single cell RNA-seq tools & ideologies will NOT translate to spatial molecular data!
genomebiology.biomedcentral.com/articles/10....
@bhuvad.bsky.social #multiomics2024 4/
Library size confounds biology in spatial transcriptomics data - Genome Biology
Spatial molecular data has transformed the study of disease microenvironments, though, larger datasets pose an analytics challenge prompting the direct adoption of single-cell RNA-sequencing tools inc...
genomebiology.biomedcentral.com
December 3, 2024 at 1:16 AM
Library size confounds biology in spatial transcriptomics data.
Single cell RNA-seq tools & ideologies will NOT translate to spatial molecular data!
genomebiology.biomedcentral.com/articles/10....
@bhuvad.bsky.social #multiomics2024 4/
Single cell RNA-seq tools & ideologies will NOT translate to spatial molecular data!
genomebiology.biomedcentral.com/articles/10....
@bhuvad.bsky.social #multiomics2024 4/