Christoph Bock Lab @ CeMM & MedUni Vienna

🤝 Great collaboration between @bocklab.bsky.social (@moritzbaio.bsky.social, Animesh, Jake), @nonchev.bsky.social, @gxxxr.bsky.social, and pathologist Viktor Kölzer.

SpotWhisperer is at #ICML25 FM4LS workshop. Visit our poster on Saturday (19 July 2025) if you're interested & attending ICML. (6/6)

🚀 Next steps: (1) Interactive SpotWhisperer web application; (2) tri-modal joint embedding of spatial transcriptomics, textual annotations, and images; (3) validation across a broad range of histopathological applications. What would you like to see? (5/6)

Molecularly informed analysis of histopathology images using natural language Histopathology refers to the microscopic examination of diseased tissues and routinely guides treatment decisions for cancer and other diseases. Currently, this analysis focuses on morphological featu...

🧑‍💻 In summary, SpotWhisperer integrates spatial transcriptomes into histopathology, bypassing high costs (we infer gene expression from H&E stains) and complexity (we built a chat interface). Check out our preprint: www.biorxiv.org/content/10.1... & website: spotwhisperer.bocklab.org (4/6)

🔍 While vision language models (VLMs) for digital pathology converse about H&E images as a whole, SpotWhisperer provides fine-grained, spot-level resolution. Consequently, SpotWhisperer outperformed SOTA VLMs (PLIP, CONCH) in the prediction of tumor regions and cell types. (3/6)

⚙️ Our SpotWhisperer method predicts spatial transcriptomes from standard H&E images with DeepSpot, and it uses CellWhisperer transcriptome-text embeddings for natural-language conversations about the cells and their transcriptomes. (2/6)

🔬 Toward histopathology 2.0: spatial transcriptomes inferred from routine diagnostic H&E images + a chat interface for cell-resolution histopathology through English language. (1/6)

🤝 Great collaboration between @bocklab.bsky.social (@moritzbaio.bsky.social, Animesh, Jake), @nonchev.bsky.social, @gxxxr.bsky.social, and pathologist Viktor Kölzer.

SpotWhisperer is at #ICML25 FM4LS workshop. Visit our poster on Saturday (19 July 2025) if you're interested & attending ICML. (6/6)

🚀 Next steps: (1) Interactive SpotWhisperer web application; (2) tri-modal joint embedding of spatial transcriptomics, textual annotations, and images; (3) validation across a broad range of histopathological applications. What would you like to see? (5/6)

Molecularly informed analysis of histopathology images using natural language Histopathology refers to the microscopic examination of diseased tissues and routinely guides treatment decisions for cancer and other diseases. Currently, this analysis focuses on morphological featu...

🧑‍💻 In summary, SpotWhisperer integrates spatial transcriptomes into histopathology, bypassing high costs (we infer gene expression from H&E stains) and complexity (we built a chat interface). Check out our preprint: www.biorxiv.org/content/10.1... and project website: spotwhisperer.bocklab.org (4/6)

🔍 While vision language models (VLMs) for digital pathology converse about H&E images as a whole, SpotWhisperer provides fine-grained, spot-level resolution. Consequently, SpotWhisperer outperformed SOTA VLMs (PLIP, CONCH) in the prediction of tumor regions and cell types. (3/6)

⚙️ Our SpotWhisperer method predicts spatial transcriptomes from standard H&E images with DeepSpot, and it uses CellWhisperer transcriptome-text embeddings for natural-language conversations about the cells and their transcriptomes. (2/6)

What excites you? What could be a great postdoc project? We are open for your ideas!

Detailed job advert: medical-epigenomics.org/files/Job_Po...
Application website: cemm.at/join-cemm/op...

YouTube video by MedUni Wien A flight through the Institute of Artificial Intelligence @ MedUni Vienna

1. More on CeMM: cemm.at/fileadmin/im...
2. And the MedUni AI Institute: www.youtube.com/watch?v=n35N...
3. Check out CellWhisperer, our AI for "talking to your data": cellwhisperer.bocklab.org
4. We like immunology: www.nature.com/articles/s41...
5. And technology: www.nature.com/articles/nme...

POSTDOC OPPPORTUNITY: We are recruiting via the CeMM postdoc program. Looking for 3 types of candidates:
1. Bioinformatics & systems biology (e.g., immunology, neurobiology or cancer)
2. ML/AI methods for biology & precision medicine
3. Technology development & bioengineering

Details below (1/3)

AI in medicine ready for takeoff 🤖🚁 We flew a drone through the Institute of Artificial Intelligence @MedUniWien. Join us for the trip and watch our team at "work". #AI #biomedicine #innovation #makingof (1/2)

Institute of Artificial Intelligence | MedUni Vienna

You can find more information about our work on the website of the @MedUniWien AI Institute: meduniwien.ac.at/ai. The full high-resolution video is also on YouTube: www.youtube.com/watch?v=n35N.... Credits: @moritzbaio.bsky.social, @rbednarsky.bsky.social, Rob ter Horst & the entire team (2/2)

AI in medicine ready for takeoff 🤖🚁 We flew a drone through the Institute of Artificial Intelligence @MedUniWien. Join us for the trip and watch our team at "work". #AI #biomedicine #innovation #makingof (1/2)

Check out the pictures & research updates of all groups at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences. Link to our Research Report: cemm.at/news/n/cemm-.... PDF: cemm.at/fileadmin/im.... Great photography by Klaus Pichler & Florian Rainer. @oeaw.bsky.social

Christoph Bock Lab - Group Picture - CeMM Research Report 2024

CeMM's new Research Report is online - a piece of art as always (link below). Each research group selected a mathematical formula that symbolizes their research and visualized it in a live-staged group picture. We picked Shannon entropy, as biomedicine is all about information (and sometimes messy)

Detailed job advert: medical-epigenomics.org/files/Job_Po...
Application website: cemm.onlyfy.jobs/job/06kmdq0b

We are searching an experienced and motivated scientist who will join the facility as a Senior NGS Technologist and take on the role of Deputy Head. The person will lead the wet lab, including NGS service delivery, assay development and validation, and support for customers and collaborators.

The Biomedical Sequencing Facility is an academic core facility and technology platform dedicated to next generation sequencing (NGS), including single-cell genomics and a wide range of other assays. It is based at the CeMM research institute on the campus of the Medical University of Vienna.

Job Posting: Senior NGS Technology & Deputy Head of the Biomedical Sequencing Facility (CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences & Medical University of Vienna)

Single-cell CRISPR screening in mouse brain - Nature Protocols Single-cell CRISPR screening is a powerful method for biological discovery. Such screens genetically perturb many genes in parallel and use single-cell RNA sequencing to assess the transcriptomic effe...

If you are considering in vivo screens - for example in mouse models of human diseases - please also have a look at our recent News&Views accompanying a very detailed and helpful protocol on that topic:
www.nature.com/articles/s41...
www.nature.com/articles/s41...

High-content CRISPR screening CRISPR screens are a powerful source of biological discovery, enabling the unbiased interrogation of gene function in a wide range of applications and species. In pooled CRISPR screens, various geneti...

Unfortunately the article is behind a paywall (no open access option provided by most review journals), but you can get a free version of the full article from the NIH PubMed Central website (thanks NIH!): pmc.ncbi.nlm.nih.gov/articles/PMC...

High-content CRISPR screening - Nature Reviews Methods Primers CRISPR screening is a high-throughput approach for identifying genes, pathways and mechanisms involved in a given phenotype or biological process. High-content read-outs of these screens, such as imag...

Could a CRISPR screen help you discover new biology? Should you consider high-content readouts such as single-cell or spatial profiling? Check out our methods primer for a hands-on guide (www.nature.com/articles/s43...), co-authored by many experts in the field & now over 225,000 views/downloads.

LAST CHANCE TO APPLY - DEADLINE 21 January 2025

The current CellWhisperer is trained on massive & well-annotated transcriptome datasets available only for human (and mouse). But less widely studied organisms may have most to gain from AI-based approaches through intelligent transfer and adaptation to the specific organism based on limited data.

Nice article about CellWhisperer – our new multimodal AI that turns single-cell RNA-seq analysis into a conversation. No coding needed, just chat in plain English. You can try it here: cellwhisperer.bocklab.org

An AI Lab Partner Helps Sift Through Transcriptomics Data Big omics datasets can be overwhelming for researchers with limited programming skills, but texting with a new AI chatbot could help them wade through their results.

Thrilled to see our work with the @bocklab.bsky.social featured in 'The Scientist'!

It's a really great read and builds on an interview I had with the @kamalnahas.bsky.social.

www.the-scientist.com/an-ai-lab-pa...