Sainsc is a new tool for efficient whole organism spatial transcriptomics data analysis at the nanometre scale. It works with Stereo-seq, VisiumHD, Xenium and Nova-ST. Looking forward to see how it works with upcoming platforms (e.g. Illumina).
github.com/HiDiHlabs/sa...

And our tireless worker bees who dedicated every Wednesday evening for 18 months for this project: Jieran Sun, Kirti Biharie, Peiying Cai, Niklas Müller-Bötticher, Paul Kiessling, Meghan A. Turner, Søren H. Dam, Florian Heyl. 🙏

I forgot the most important bit! This would not have been possible without the wonderful and amazing SpaceHack community. Special shout outs to Brain Long, Ahmed Mahfouz and @markrobinsonca.bsky.social for their work, ideas and resources...

We wrap up our analysis framework into SACCELERATOR, github.com/SpatialHacka..., and present two case studies on brain and colon cancer datasets to remind people that having domain expertise and performing interactive analysis is more important than picking the "best" tool.

General findings:
- benchmarking studies can be inconsistent
- methods do not scale to new datasets
- "ground truths" do not consider granularity of biological features
- looking at the differences between methods (entropy) is informative
- method performance doesn't match subjective importance

We also released the ovrl.py tool to identify areas of cell overlaps in imaging-based spatial transcriptomic data (e.g. #Xenium, #MERSCOPE, #cosMX).
GitHub: github.com/HiDiHlabs/ov...

We also sneak in a python implementation for the spatially aware MULTISPATI-PCA. We think this should pretty much replace "non-spatial" PCA for all spatial modalities in most cases.
GitHub: github.com/HiDiHlabs/mu...
RtD: multispaeti.readthedocs.io/1.0.0/genera...

SpatialLeiden integrates with the #scverse by leveraging #scanpy and #anndata but can also be used independently.
GitHub: github.com/HiDiHlabs/sp...
RtD: spatialleiden.readthedocs.io/stable/

The HISTOMAP projects aims to use AI and spatial transcriptomics data to accelerate biomarker detection for bladder cancer. We will work closely with the clinic, pathology, and regulatory experts to investigate how best to get these models into clinical routine.

I tried Sainsc for our MERSCOPE data and Naveed, it works wonderfully! Importantly, the documentation is excellent. Thank you so much for the clear tutorial and explanations. This is truly a life saver for my analysis at the moment. Props to the team, this is awesome work!

Am I really the first to repost Mats Nilsson? What an honour!

SpatialLeiden adds spatial support to the Leiden clustering algrithm. It has 3 parameters. Two we know from scRNAseq analysis (resolution and num of neighbors), and the other is the weight of the spatial info. We thin it is the natural choice for spatial clustering for the single-cell community!

... we will also implement multi-omics and multi-sample support at #SpaceHack spatialhackathon.github.io