CODI

By ONI (Oxford Nanoimaging)

Acquisition, analysis and reporting in one place Flexible software for every environment Sample to answer CODI is a comprehensive software solution with automated image acquisition, analysis and reports anyone can use Flexible data access CODI runs in the cloud to allow analysis from everywhere, or offline to support local data and instrument control Analysis & reporting simplified Analysis app workflows can be customized to analyze hundreds of datasets and generate reports with ease Sharing and collaboration CODI cloud makes it easy to organize datasets and analyses into collaborations and instantly share them with collaborators. One platform, two ways to work CODI cloud CODI offline Analyze your data, your way Use CODI in the cloud or offline to acquire, analyze, organize, and report your data. Save analysis settings for specific experiments and apply them to newly acquired datasets to support reproducibility. Easily organize, analyze, and export images and reports. CODI cloud enables streamlined analysis, collaboration, and access from anywhere, while CODI offline runs locally in restricted-connectivity or air-gapped environments. What’s in CODI CODI space Datasets & collaborations Analysis workflows Share & export results With CODI you are able to Understand the morphology of my structure Understand how my molecules of interest organize Clean up my data to improve signal-to-noise ratio Identify EV subpopulations based on size or biomarker content Understand the morphology of my structure Single-molecule localization microscopy techniques, such as dSTORM, PAINT or PALM, pinpoint the position of individual molecules, providing morphological information of structures and the organization of proteins. To assess the distribution of a specific protein within a structure, a simple density profile measurement can be performed. 3D imaging and visualization further enhances the nanoscale information of structure morphology and protein organization. Understand how my molecules of interest organize One of the most powerful applications of SMLM is investigating spatial distributions down to the nanometer scale. The raw point cloud of localizations serves as the basis of nanoscale morphological analysis. CODI offers different clustering analyses including DBSCAN and our in-house extension of HDBSCAN called Constrained Clustering. Clustering on localization data allows researchers to find biological structures and quantify their morphological properties (size and shape), as well as determine presence or absence of specific markers of interest. Clean up my data to improve signal-to-noise ratio A critical part of SMLM imaging is removing noise to obtain accurate information and sensitivity for the analysis. To this end, the CODI analysis workflow includes a single-molecule filtering step that enables real-time visualization as users tune the filtering parameters, as well as default filters that serve as a great starting point for keeping only the most accurate data. Identify EV subpopulations based on size or biomarker content The EV Profiling App on CODI is the perfect analysis workflow for EV samples with various subpopulations, allowing you to quantify size and biomarker distributions from a collection of single EVs. The App includes a range of tools from drift correction, single-molecule filtering, clustering, cluster filtering, and counting of biomarker distribution. In addition, the batch analysis tool allows analysis automation by applying the same analysis settings to multiple datasets. CODI Apps CODI contains several app workflows to streamline and simplify single molecule data analysis. Each workflow is a unique combination of tools for a specific kind of dataset, all starting with the basics of spatial drift correction and single-molecule localization filtering.