How to guide: CODI Apps and Batch Analysis

How to guide: CODI Apps and Batch Analysis

Tool view


Purpose of the tool

CODI Apps operate within a new analysis ecosystem, an enhanced version of the platform. Each App contains a set of powerful analysis tools that enable scientists to create, save and run end-to-end batch analysis workflows. The new App ecosystem allows the constant integration of new analysis tools and the growth of a collection of CODI Apps containing custom analysis workflows to fulfill different research needs. 


Contents 

  • What can CODI Apps do?

  • Definitions: Apps, Settings, Results & Batch Analysis

  • 2023 CODI Analysis Apps

  • Getting started with Apps and settings menu 

  • Running Analysis tools

  • Creating new results and Saving new settings

  • Loading parameters

  • Favorite settings

  • Non-operational tools

  • Running Batch Analysis

What can CODI Apps do?


CODI Apps can be used to: 

  • Correct for spatial drift and filter localization data

  • Characterize the morphology of samples and resolve proteins at the nanoscale

  • Explore the spatial distribution of molecules (clustering, size, spacing)

  • Quantify the amount of molecules in an image or the ratio of multiple molecules

  • …and more to come!


CODI Apps include ONI’s default settings to guide users through basic single molecule analysis. We recommend using default App settings first and tweaking the parameters to fit each dataset; then save and re-use on other dataset individually or using the new Batch Analysis tool. 


Definitions: Apps, Settings, Results & Batch Analysis


Apps: A chain of analysis tools.

CODI analysis Apps include a sequence of fixed tools. Use the App that better matches your analytical needs.  

Settings: Settings for a CODI App that can be applied to datasets.

Default settings from a list of ONI (ONI App settings templates) or user-defined settings can be selected. Settings from collaborators can be used. Start analysis on a single dataset or run batch analysis.

Parameters can be changed and Apps settings saved to re-apply to other datasets.

Results: CODI App with settings applied to a dataset creates a result. Results can store any custom parameters that diverge from initial settings and analysis results. 

These can be created from:

  • A single dataset for single dataset analysis

  • Multiple datasets through batch analysis

The latest CODI ecosystem offers the ability to apply and switch between multiple analysis pipelines on the same dataset. 


What else is new?

  • Fast-forward: Select an App and default settings, then apply all the analysis workflow at once on a dataset using the fast-forward tool (see Running analysis tools section). This will allow you to quickly apply an analysis to your dataset. 

  • Batch Analysis: Select multiple datasets within a collaboration and apply simultaneously an analysis App and App settings to all datasets. Follow the batch processing progression and visualize your results when done. 


2023 CODI analysis Apps

As a starter package, ONI offers a set of 4 Apps. More CODI Apps will be released during 2023!

Data clean-up App:

This App allows the correction of residual spatial drift in single molecule localization data without fiducial markers. It enables filtering of individual localizations and the use of the temporal grouping tool to reduce noise. Use this App to capture and visualize super-resolution images and export high resolution versions for publication or analysis.

Nanoscale Morphology App: 

This App allows the correction and filtering of data and the extraction of morphological features, biological structure or proteins of interest within a sample using the annotation tool.


dSTORM (cell) App: 

This App provides a cell-based dSTORM analysis workflow from filtering to clustering.

dSTORM (default) App: 

This App provides a complete single molecule localization microscopy analysis workflow. It includes all the tools available on the former CODI analysis platform.


EV App: Coming soon! 

dSTORM analysis workflow adapted to EV datasets. It can be used to quantify biomarkers in a given sample and quantify the  distribution of molecules across a sample for comparison in an experiment.


Legacy analysis 


Retrieving old dSTORM analysis (i.e. prior CODI Apps release, 01-2023) can be done by switching the view from results view to the legacy analysis execution view. Former executions can be retrieved from the list on the info page or from the results menu of the collaboration.



**Important note: any previously run executions cannot be migrated to the new CODI Apps format. This means that analysis will have to be done using CODI Apps. Similarly, analysis performed using CODI Apps cannot be migrated to the former analysis execution format. The new model integrates an entire new code base architecture that renders complex any migration. We understand the inconvenience caused by this and apologize for any trouble. We have worked hard to deliver a new and improved ecosystem that is highly modular, scalable and full of potential for delivering future CODI Apps to help support user needs.** 


             
     
Getting started with Apps and settings menu  
To begin an analysis, click the App and settings menu accessible from a dataset info page or dataset view (see screenshots below). 



When the App and settings menu appears, select a CODI Analysis App that will satisfy your biological questions. For more information on each App, see description. 


Once the App is chosen, select the App settings among a list of ONI template settings as a guide across the data analysis journey. Alternatively, user-defined settings saved by the user or the App default settings (all filters and algorithm parameters to default values) can be used. 



Results of analysis previously applied to datasets can be accessed under the “Results” tab. An analysis can be triggered by selecting a preferred App and settings pinned as “Favorite” under the “Star” icon tab (see Favorite parameters section). 

Running Analysis tools 

Once an App and settings are selected, an analysis tab opens on the left-hand side menu of the dataset view, this is a “Result”. As many analysis tabs as needed can be opened by selecting a different App or the same App with different settings (see screenshot below). Close, expand, navigate through multiple analysis tabs without quitting your current analysis is possible now with the new CODI analysis ecosystem.



Using the Analysis tab, analysis tools can be run one by one either sequentially or by navigating to a specific tool. Note that running a tool will run the algorithm or filters with the default settings automatically. Similarly, running a specific tool will automatically apply all the up-stream tools with default settings unless settings have already been edited. 

To apply all the analysis tools with default/saved settings at once, click on the Fast-forward button (see screenshot below). Then, visualize in one click the application of an analysis workflow on your dataset. This feature will save time and help you in your day to day analysis routines. 

Creating new results and saving parameters 

Parameters can be adapted to each dataset at any time and deviate from the default settings of an analysis App. This will result in a new result. Tweaking any parameters from any tool will generate a new analysis tab from which all parameters can be changed (see screenshot below). 



Once all new parameters are defined and applied for each tool, the new settings can be saved and named, and will appear on the App and settings menu. 

Loading parameters 

From each individual tool, specific parameters can be loaded by clicking on the loading settings button (see screenshot below). 



Favorite parameters 

App settings can be defined, tagged or untagged at any time as favorite by clicking on the “star” icon. Retrieving favorite settings can be done from the favorite tab of the App and settings menu. 

Non-operational tools

Toggle on/off a tool to “declare” it non-operational in its analysis flow. This allows you to run a whole analysis App with default settings by omitting some tools from the same analysis App. This function can ease the analysis and exploration journey. For the time being, only the drift correction and temporal grouping tool can be set as non-operational. 


Running Batch analysis 

Apply a CODI App with its settings to multiple datasets, and perform batch analysis. Batch analysis can be triggered via the collaboration directly or after run-all analysis on an individual dataset (see screenshots below).




Once an App and its settings are selected from the menu or directly via a single analysis, select datasets to apply the batch analysis (see screenshot below).





Then, visualize batch analysis progress and access the results from the collaboration result view page (see screenshots below). 




Exporting results 

After a single or batch analysis, dataset results can be exported from the collaboration results view. CODI will aggregate all results generated by the selected datasets into a .csv file by file type, the files are exported into a .zip file (see screenshots below). Note that CODI only generates files if they exist (positivity results, summary report, clustering results).

To access this feature, navigate to the results view and click on “batch download”. 



From this datasets results list:
Click to select dataset results or click “select all”
Click on “download results” to download .csv files
Results are automatically exported on a .zip file. 



Results of analysis previously applied to datasets can be accessed under the “Results” tab. An analysis can be triggered by selecting a preferred App and settings pinned as “Favorite” under the “Star” icon tab (see Favorite parameters section).




Running Analysis tools 

Once an App and settings are selected, an analysis tab opens on the left-hand side menu of the dataset view, this is a “Result”. As many analysis tabs as needed can be opened by selecting a different App or the same App with different settings (see screenshot below). Close, expand, navigate through multiple analysis tabs without quitting your current analysis is possible now with the new CODI analysis ecosystem.


Using the Analysis tab, analysis tools can be run one by one either sequentially or by navigating to a specific tool. Note that running a tool will run the algorithm or filters with the default settings automatically. Similarly, running a specific tool will automatically apply all the up-stream tools with default settings unless settings have already been edited. 


To apply all the analysis tools with default/saved settings at once, click on the Fast-forward button (see screenshot below). Then, visualize in one click the application of an analysis workflow on your dataset. This feature will save time and help you in your day to day analysis routines.

Creating new results and saving parameters 


Parameters can be adapted to each dataset at any time and deviate from the default settings of an analysis App. This will result in a new result. Tweaking any parameters from any tool will generate a new analysis tab from which all parameters can be changed (see screenshot below). 




Once all new parameters are defined and applied for each tool, the new settings can be saved and named, and will appear on the App and settings menu. 


Loading parameters 


From each individual tool, specific parameters can be loaded by clicking on the loading settings button (see screenshot below). 


Favorite parameters 


App settings can be defined, tagged or untagged at any time as favorite by clicking on the “star” icon. Retrieving favorite settings can be done from the favorite tab of the App and settings menu. 


Non-operational tools


Toggle on/off a tool to “declare” it non-operational in its analysis flow. This allows you to run a whole analysis App with default settings by omitting some tools from the same analysis App. This function can ease the analysis and exploration journey. For the time being, only the drift correction and temporal grouping tool can be set as non-operational. 


Running Batch analysis 


Apply a CODI App with its settings to multiple datasets, and perform batch analysis. Batch analysis can be triggered via the collaboration directly or after run-all analysis on an individual dataset (see screenshots below).




Once an App and its settings are selected from the menu or directly via a single analysis, select datasets to apply the batch analysis (see screenshot below).

Then, visualize batch analysis progress and access the results from the collaboration result view page (see screenshots below).



Exporting results 


After a single or batch analysis, dataset results can be exported from the collaboration results view. CODI will aggregate all results generated by the selected datasets into a .csv file by file type, the files are exported into a .zip file (see screenshots below). Note that CODI only generates files if they exist (positivity results, summary report, clustering results).

To access this feature, navigate to the results view and click on “batch download”.

From this datasets results list:

  1. Click to select dataset results or click “select all”

  2. Click on “download results” to download .csv files

  3. Results are automatically exported on a .zip file.



    • Related Articles

    • 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 ...

    • CODI license

      CODI, including it’s design, source code, analysis tools, and other associated material is protected under Copyright. Public datasets on CODI are published under the Creative Commons Attribution-ShareAlike 4.0 license.

    • 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: 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, ...

    • 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 ...