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CODI
Analyze, collaborate, and store using our cloud-based software
Key Features
With CODI you are able to
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.
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.
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.
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.
What’s in CODI?
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.
The Clustering App provides all of the necessary analysis widgets for cell-based clustering analysis workflow.
Key outputs:
- Real-time data visualization, including histograms of various cluster metadata
- Clustering CSV containing quantitative and morphological information about each cluster
- High-resolution images of single molecule localization and their assigned clusters
The Clustering & Counting App provides a complete single-molecule localization microscopy analysis workflow. It includes all the widgets available on Clustering App and a Counting widget.
Key outputs:
- Real-time data visualization, including histograms of various cluster metadata
- Clustering CSV containing quantitative and morphological information about each cluster
- High-resolution images of single-molecule localization and their assigned clusters
- Summary report segmenting clusters into user-defined phenotypes
The EV Profiling App is the perfect analysis workflow for Extracellular Vesicles (EV) datasets. It contains a set of algorithms customized for quantifying size and biomarker distributions of single EVs in a sample.
Key outputs:
- Real-time data visualization, including histograms of various EV metadata
- Clustering CSV containing quantitative and morphological information about each EV
- Summary report segmenting EVs into user-defined phenotypes
- High-resolution images of EVs and their single molecule localizations
CODI Support
FAQs
No. Everyone using a Nanoimager gets access to CODI and its applications at no charge during the Beta phase of release.
Technically it can, however, it is currently designed to support data acquired from the Nanoimager.
No. CODI fully runs on the cloud, so you can do your analysis anywhere. The software to run the Nanoimager (currently NimOS) works on most modern computers, running 64-bit Windows 10. We supply a high-specification laptop with each Nanoimager and this is included in the price.