How to analyse data in CODI?

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 NimOS or other software of your choice.   

Intro and keywords

It is possible to analyse data that you have uploaded, or data that someone lese uploaded and shared with you or data that are publicly available. 
CODI analysis work through  Apps  which are sets of tools put in a specific order and can be seen as workflow. Each App can be either specific to an application, a sample or a type of analysis.
Some tools can't be skip and that is why two apps can look very similar with only different tool. 

Each App also has   Settings , which are parameters used by the tools, such as filters. Every App has some default settings, but those can be modified during the analysis and then saved to be reused on another acquisition or through batch analysis. 

With the advantage of being online, it is possible for ONI to develop new tools and new apps and add them over time. 

Analysis 

Once you have selected the data to analyse, click on the analysis button on the left side. 


This will open the Apps tab where you can choose the appropriate type of analysis. 



As of February 2024, CODI has 3 Apps with the following default settings
  1. Clustering 
    1. Clustering essential
    2. dSTORM training kit - Those settings need to be used with the dSTORM training kit available on our online store. 
    3. Discovery kit: dSTORM clustering essential
  2. Clustering and counting 
    1. Counting essential
    2. Discovery kit: dSTORM clustering essential
  3. EV profiling 
    1. EV profiling essential - those settings should be use for EV data taken with our EV profiler kit, but can also be modified to accommodate other EV experiment 

Small FAQ: 

When should I use Clustering or Clustering and counting? 

After clustering, the counting tool will count the number of localisation for every channel in every cluster. This is helpful for an application where knowing if the clusters are single, double or triple positive and what is the ratio of each channel in the cluster. 

What is the difference between the Essential and Discovery kit essential? 

The discovery kit essentials have more specific and stricter filters. This is because our Discovery kit comes with labeled secondary antibody that we have characterise and known filters parameters. 

Where can i learn more about each tool? 

Please refer to specific tool page to know more about each of them 


    • Related Articles

    • Data Metadata

      Two ways to read the metadata of the current data: Either click on Data > View Acquisition Data to show the metafile: Or open the corresponding "acq.nim" file to show the metadata:

    • Data Interpretation

      The output format varies depending on how the acquisition is performed: Normal Acquisition Normal acquisition refers to taking images without using any advanced features (e.g. light program). Normally each normal acquisition generates 8 files: .locb: ...

    • Data Import

      Instructions: In Analyze, click on Load Data. Navigate to the folder of interest and select either the Tiff file or the Locb File to import. Discussion: If the dataset is modified via 3rd party software such as ImageJ, it may not be compatible with ...

    • Data Export

      There are different ways to save/export data from NimOS: Copy To Clipboard (Raw) Instructions: Right-click on any of the channels and click on Copy To Clipboard: Paste it into any other data viewer (e.g. ImageJ, Paint, Excel...) to visualize and save ...

    • CODI-FAQ

      What is CODI ? Our CODI cloud platform is a beta and is currently an analysis platform used for the analysis of data acquired by our Nanoimager and its local acquisition software (NimOS). CODI is... A collaborative platform to share your data and ...