How to guides
How to guide: Counting tool
Tool view Purpose of tool Counts the number of localisations or ‘bins’ by channel around a set of centre points - currently the centroids of a clustering result. Contents Inputs Results Outputs Inputs The centre points for counting come from a loaded ...
How to guide: Filtering tool
Tool view Purpose of tool Enable user to filter out points based on their properties and save the output for further analysis in workflow. Contents Input parameters Multiple channels Output results Input parameters The points in dSTORM acquisitions ...
How-to-guide: Temporal grouping tool
Tool view Purpose of tool In localisations-based super-resolution microscopy, each fluorescent molecule can emit ("blink") multiple times, depending on its properties and the super-resolution technique used. Those blinking events are localized ...
How to guide: The CODI Desktop Uploader
Tool view Purpose of tool The CODI Desktop Uploader is a tool created to ease the transition between NimOS and CODI. The main objective of the application is to facilitate the uploading of NimOS generated datasets to the CODI cloud platform. It ...
How to guide: Clustering tool
Tool view Purpose of tool The tool performs clustering on localisation data to find biological structures and quantify their statistical and morphological properties. The default clustering method is HDBSCAN. The cluster results can then be ...
How to guide: CODI Apps and Batch Analysis
Welcome to CODI Apps and Batch Analysis CODI Apps and Batch Analysis is an enhanced version of the CODI platform that unlocks faster and more customized analysis pipelines. Each App contains a set of powerful analysis widgets that enable scientists ...
How to guide: Getting started
Welcome to CODI! This article explains how to navigate into CODI CODI home page The CODI home page shows a gallery of datasets. At any point, it is possible to return to this page by clicking on the CODI logo in the top left of the page. Creating an ...
How to analyse data in CODI?
First, for the moment CODI is only able to display super-resolution microscopy data, meaning images create from localisations of blinking event. For the visualisation or analysis of raw images, such as brightfield, widefield or tracking, please us ...
How to guide: Drift correction
Tool view Purpose of tool This tool attempts to correct for the drift that occurs during an acquisition. Without this correction the resolution of the sample is degraded which will affect visual quality as well as downstream analysis. The drift ...
How to guide: Visualization panel
For the moment CODI is only able to display super-resolution microscopy data, meaning images create from localizations of blinking event. For the visualisation or analysis of raw images, such as brightfield, widefield or tracking, please us NimOS or ...
How to guide: Annotation tool (ROI)
Purpose of tool Select regions of interest (ROIs) in images. While multiple ROIs can be drawn, s How to draw ROIs To begin drawing an ROI, click on one of the three green button depending on the shape you would like to draw. For the polygon: Click on ...
How-to-guide: How to share and organize your data
Tool View Purpose of tool CODI is a Collaborative Discovery platform to share your data and analyses with colleagues and the public, opening up new possibilities for cross dataset insights. Using our tool Collaborations you will be able to organize, ...