Cell Maps for Artificial Intelligence (CM4AI) will deliver machine-readable hierarchical maps of cell architecture as AI-ready data, together with quarterly data releases of map-input data streams. CM4AI cell maps are produced from multimodal interrogation of chromatin modifiers, metabolic enzymes, and other proteins involved in cancer, neuropsychiatric, and cardiac disorders in disease-relevant cell lines under treated and untreated conditions, utilizing state-of-the-art mass spectrometry-based proteomics, spatial proteomics / cell imaging, and genetic perturbations via CRISPR/Cas9. CM4AI is a collaboration of UCSD, UCSF, Stanford, UVA, Yale, UT Austin, UA Birmingham, Simon Fraser University, and the Hastings Center, as part of the NIH Bridge2AI program.
Data Insights
Explore the numbers behind our innovative data generation project and see the impact we are making.
Protein Interactions
1,374
Immunofluorescent Images
53,788
Total Proteins Investigated
7,023
genes targeted
11,739
Data volume
21.4 TB
CM4AI’s Flagship Datasets
We are generating deep multi-modal data for a shared list of proteins across all cell types and treatment conditions to achieve an unparallelled level of biological insight
Curated dataset for undifferentiated (parental) iPSCs and iPSC-derived neural progenitor cells (NPCs), neurons, and cardiomyocytes include:
• Perturb-seq of >11,000 genes (whole-genome)
• SEC-MS capturing ~7,000 proteins
• IF images (coming soon!)
Curated datasets for TNBC cells under untreated (DMSO control), vorinostat, and paclitaxel conditions include:
•SEC-MS capturing ~7,000 proteins
•IF images for 523 proteins
•Perturb-seq of 200 genes
•AP-MS interactomes (coming soon!)
Our latest data release
This repository is under review for potential modification in compliance with Administration directives.
June 2026 Data Release (Beta)
doi.org/10.18130/V3/HIGT4C
This dataset is the June 2026 Data Release of CM4AI, the Functional Genomics Grand Challenge in the NIH Bridge2AI program.
Released on:
June 17, 2025
Frequently Asked Questions
CM4AI releases data quarterly, ensuring continuous updates to the cell maps and input data streams.
CM4AI provides hierarchical cell maps derived from various data streams, including:
• Mass spectrometry-based proteomics
• Spatial proteomics and cell imaging
• Genetic perturbations using CRISPR/Cas9
These datasets focus on chromatin modifiers, metabolic enzymes, and other proteins linked to cancer, neuropsychiatric, and cardiac disorders.
We use a combination of mapping techniques such as proteomic mass spectrometry, cellular imaging, and genetic perturbation via CRISPR/Cas9 to create a library of large-scale maps of cellular structure and function. These maps are then organized and made available for use in our Data Releases.
