Image Analysis & Visualization Software

The LSP develops open-source software tools that improve the reproducibility, accuracy, and accessibility of spatial biology datasets.

Spatial biology methods like highly-multiplexed tissue imaging make it possible to visualize the precise locations of 60-100 proteins within human tissues. The resulting images contain deep biological insights, but their size - which can be 200 GB to 1 TB - makes them challenging to analyze and share. 

LSP investigators have developed numerous open-source software solutions that address these persistent challenges. These include tools for identifying single-cell boundaries (a process known as segmentation), performing quality control, analyzing the single-cell data, and visualizing tissue images online (Minerva). Many of these tools have been integrated into MCMICRO, a customizable software pipeline that is used by labs across the globe. 

LSP investigators are collaborating with external communities (like nf-core and the NCI Imaging Data Commons) to integrate our software packages into standardized infrastructures. We aim for our software tools to ensure precise and reproducible tissue imaging datasets so that the deep molecular insights within spatial datasets can be fully realized.