Technology Development

Technology Development

Biological Imaging Development

The BIDC is building out a spatialtranscriptomics microscope suitable for multiple technologies and workflows. Currently, the system can perform ZipSeq experiments where the user utilizes a graphical user interface (GUI) to define regions of interest and the oligonucleotide labeling sequences. Additionally, a plugin has been written to automatically scan 10x Genomics Visium slides and package the data for downstream analysis. The microscope is open to Beta users, and we welcome feedback on ways to improve and expand the platform.

Data Science

We are building the UCSF Data Library platform to store, curate, analyze and share high-dimensional data. We are also developing methods and building pipelines for analysis and visualization of single-cell data.

As a cross-CoLabs team (working with D2B and BIDC) we have developed the Cyclone pipeline, an accessible method for the clustering and optimization of cytometry data. Preprint available here, code available on our GitHub.

Disease to Biology

We have acquired the S2 Genomics singulator, an instrument that enables reproducible, rapid, and hands-off tissue dissociations into single  nuclei suspensions from frozen tissue for downstream snRNAseq pipeline. See it here.   Please contact Alexis Combes if you are interested in using the instrument. 

We have established a pipeline to perform multimodal single-cell genomics on frozen biopsies on a variety of tissue including skin, salivary gland colon, and more. This work was supported through our AutoIPI consortium project.

We will acquire the CosMx Single-cell transcriptomic platform: Spatial molecular imager,  which will be installed in D2B in the fall of 2023. This equipment will be accessible to the UCSF research community to perform single-cell transcriptomic assays on FFPE tissues.  Please contact Alexis Combes if you are interested in using the instrument. 


Flow Cytometry

We are developing methods for operation, sample processing and data generation using the state-of-the-art Ionpath MIBIscope, from backbone panels to an analytical pipeline to decrease barrier of entry to this new technology.

We are testing and implementing newly developed standardization methods for analysis of small particles microvesicles and exosomes using the full spectrum Cytek Aurora flow cytometer analyzer.


The Genomics CoLab is working to integrate novel methods of spatial transcriptomics into our collaborative and core projects. We currently support the 10x Genomics CytAssist enabled Visium platform which allows for transfer of existing FFPE and Fresh Frozen slides to Visium slides for spatial resolved whole transcriptome data at a resolution of ~100um. 

In partnership with the Disease to Biology CoLab we are bringing in two additional, subcellular resolution platforms: The 10x Genomics Xenium and Nanostring CosMX. We are also involved in a cross CoLabs collaborative effort to evaluate data from each of these platforms to provide evidence-based suggestions on which platform may best suit each project and develop an analysis toolkit for this emerging technology. 

Additional technological development underway include automating multiple NGS methods on our recently purchased BioMek i7. Through this new liquid handler, we expect to offer automated solutions to single cell RNA-seq, low input and degraded RNA-seq methods, ATAC-seq and more. 

Learn about CoProjects, Incubators, and Plug-in Labs

CoProjects are a series of shared projects designed to integrate our community through common pipelines and data curation. CoLabs CoProjects aim to build immune profiles for untapped streams of human diseases at UCSF.