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.

Disease to Biology

We are developing  SCENITH, a method a flow cytometry-based method that will be used to profile metabolic states of infant immune cells in tumor biopsies (Arguello RJ, Combes AJ, et al Cell Metabolism, 2020).

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.


Developing automated methods of bulk RNA-seq library preparation in miniaturized, 384 well formats to decrease cost and increase throughput.

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.