How to guide: CODI Apps and Batch Analysis

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 to create, save and run end-to-end batch analysis workflows. The new App ecosystem allows constant integration of new analysis Apps, and the collection of CODI Apps will continue to grow, making super-resolution analysis faster and easier for everyone.

Contents 

  • What can CODI Apps do?

  • Definitions: Apps, Settings, Results & Batch Analysis

  • 2023 CODI Analysis Apps

  • Finding Previous Analysis - Legacy Analysis 

  • Getting Started with Apps and settings menu 

  • Running Analysis Widgets

  • Creating New Results and Saving New Settings

  • Loading Individual Analysis Widget Parameters

  • Saving Analysis App Settings for Re-use as Favorites

  • Disabling / Skipping Steps

  • Running Batch Analysis

  • Exporting Results

What can CODI Apps and Batch Analysis do?

CODI Apps and Batch Analysis can be used to: 
  1. Quantify statistical and morphological properties of your data.
  2. Explore subpopulations and quantify statistical and morphological properties of your data. 
  3. Quickly identify subpopulations with single EV precision with a customized EV workflow.
  4. … and more to come soon!
CODI Apps and Batch Analysis 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 individual datasets or use the new Batch Analysis widget to apply the settings to multiple datasets in a collaboration.

Definitions: Apps, Settings, Results & Batch Analysis

App

Settings

Results

A chain of analysis widgets

App + app parameters

App + settings + dataset


App : CODI analysis Apps are sequences of widgets chained together and designed to be executed together. Use the App that best matches your analytical needs.

Settings : Settings are the combination of all of the parameters in each analysis widget of a CODI App. Default settings from a list of ONI App Settings Templates or User-Defined Settings can be selected, and these parameters can be changed and saved for further use on other datasets.

Results: Applying settings to a CODI analysis App workflow creates an analysis Result. Results store any custom parameters that diverge from initial settings and analysis results. A new result is created each time an App workflow is run on a dataset.

The latest CODI ecosystem offers the ability to apply and switch between multiple analysis Apps and Results on the same dataset, so you can easily compare between analysis conditions.

What else is new?

Fast-forward

Complete your analysis with 1 click. Select an App and default settings, then apply all the analysis workflow at once on a dataset using the fast-forward widget (see Running analysis widgets section). 

Batch Analysis

Analyze all multiple datasets at once. Select multiple datasets within a collaboration and apply an analysis App and App settings simultaneously to all datasets. Follow the batch processing progression and download the results from all of your datasets in a single file. 

2023 CODI Analysis Apps

As a starter package, ONI offers a set of 3 Apps. More CODI Apps will be released during 2023!


Clustering App: 

The Clustering App provides all of the necessary analysis widgets for a cell-based clustering analysis workflow.


Clustering & Counting App: 

The Clustering & Counting App provides a complete single molecule localization microscopy analysis workflow. It includes all the widgets available on the former CODI analysis platform, including the Counting widget.


EV Profiling App:  

The EV Profiling App is the perfect analysis workflow for EV datasets. It can be used to quantify size and biomarker distributions of single EVs in a sample.

Don’t know where to start? 

The Clustering & Counting app provides all of the same functionality that you were used to in CODI before this update.

Finding Previous Analysis - Legacy Analysis 

Even with the power of CODI Analysis apps, we want to make sure you can still access your previous analyses, which we’re now calling “Legacy Analysis.”

Retrieving old Clustering and Counting analysis (i.e. prior CODI Apps and Batch release, June 2023) can be done by switching the view from App analysis results view to the Legacy analysis results view. Previous analyses can be retrieved from the list on the info page or from the results menu of the collaboration.


Important note: Any previously run analysis “executions” cannot be migrated to the new CODI Apps format. Apps format, and must be reanalyzed to benefit from new features like Batch Analysis. Similarly, analysis performed using CODI Apps cannot be migrated to the former analysis execution format. 
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  

Step 1. Start an Analysis App on your dataset.

To begin an analysis, open a dataset and click the “Add a new analysis tab” button 

Step 2. Select the Analysis App that fits your workflow. 

For more information on each App, see its description, and hover over an app to preview the widgets in its workflow. 

Step 3. Choose from default or customized settings

These settings contain a set of parameters for each widget in your app workflow and are a starting point on your data analysis journey. They can be adjusted at any time during analysis. 
The App Settings list contains ONI template settings as well settings that you name and mark as favorite for future use.
The app “Essentials” settings are usually a good place to start.

Step 4. Proceed through your analysis step-by-step or use the fast-forward button to run all steps with a single click.

See the next section, Running Analysis Widgets, for more details on running your analysis.
Once you’re done adjusting your settings for analysis, you can save them as a favorite by clicking on the “fast-forward” button, giving them a name and clicking the star button.

Done! Each time an Analysis app is run, a new result is created

You can access results of analysis previously applied to this dataset 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 Widgets 

Once an App and settings are selected, an analysis tab opens on the left-hand side menu of the dataset view. App workflows are displayed as a vertical list of sequential steps, and clicking on a step opens its corresponding widget.

Multiple analysis tabs can be opened by selecting a different App or the same App with different settings (see screenshot below). Close, expand, and navigate through multiple analysis tabs without quitting your current analysis with the new CODI Analysis App ecosystem.

CODI Analysis Apps provide flexibility when running Analysis workflows:
  1. One Step: Analysis widgets can be run sequentially, stepping through each widget linearly and using the “run” button in the top left of each widget.
    The first time you’re running an analysis, we suggest running each app individually and then proceeding to the next widget in the app workflow, in order to visualize the effects of each analysis widget.
  2. Several Steps: Partial analysis workflows can be run by selecting any step in the workflow and running that widget. Doing so will run all widgets above (sequentially before) as well as the current widget.
    Run several steps when you’re confident your analysis settings are good for previous steps in the workflow, but you might want to change some parameters of the current one.
    For example, if you want to see how changing temporal grouping filters affects your dataset, navigate to the Temporal Grouping widget, click play, and then set your filters.
  3. All Steps: Click the “Fast Forward” button to run all of the steps in a workflow with the settings you have selected or modified.
    This is the fastest way to analyze your datasets when you are confident of the settings that you’ve chosen.

Creating New Results and Saving Settings 

CODI Apps and Batch Analysis brings powerful new capabilities, such as the ability to test various analysis Settings to help understand the effects of parameters on your datasets.

Once you have successfully run an analysis step or en tire analysis App workflow and you modify any of the steps in the workflow, a new “branch” will be created from the previous result, allowing you to further tweak your settings. Once you run that new analysis workflow, you will create a new result with the new settings that you can compare to your previous result, if desired.

When initiating an analysis branching, you will see a small window for a few seconds that allows you to “go back” to your previous settings. Once the branching is complete, you can access your previous results from the result list on the dataset info page.



When you’re done tweaking settings and running the analysis workflow, these analysis settings can be  and named, and will appear on the App and settings menu. 

Saving Analysis App Settings for Re-use as Favorites

Retrieving favorite settings can be done from the favorite tab of the App and settings menu.

Loading Individual Analysis Widget Parameters 

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

Disabling or Skipping Analysis Steps 

With CODI Apps and Batch Analysis, we are introducing the concept of analysis workflows as linear sets of analysis widgets, but we realize that this doesn’t fit every workflow.
While we are working on improving the experience, certain widgets can be skipped by setting custom settings on the “back” of the widget (accessed through the “...” button in the top right corner of the widget:

Drift Correction

Click the “Drift Correction Method” button (button in the lower-right hand corner of the button group) until you’ve selected “None”.

Temporal Grouping

Change the “frame gap” to “-1”.


Running Batch analysis 

Once you have established optimal settings for your data, CODI Apps and Batch Analysis now lets you apply any analysis App and Settings to all of your datasets in any collaboration with Batch Analysis. 

There are 2 ways to run a batch analysis:

From an Analysis App:

When you’ve completed an analysis app workflow, you can use the same settings that you just applied to the current dataset in a batch analysis across any dataset by clicking on the fast forward button and then “use settings in batch analysis”.

Select the collaboration containing the datasets you want to analyze, and you will be taken to the batch analysis page from a collaboration.  

From a collaboration:

  1. On any collaboration page, click the “start a batch analysis” button
  2. Select the Analysis App and Settings you want to use for your batch analysis.
  3. Select the datasets you want to apply these Apps and Settings to.
  4. Click the green “Run Batch on datasets” button to start batch analysis.
  5. You will be taken to the collaboration result view, where you will be able to follow the progress of the analyses on all your datasets.



You can return to this collaboration results view at any time by clicking the “results view” button on a collaboration info page.

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 for each kind of file (clusters, summaries, etc). The files are exported as a .zip file (see screenshots below).

CODI only generates files if they exist for the analysis results that you've chosen.  If you choose to batch download results from different apps, CODI will aggregate all the results into 1 batch positivity results, summary report, and clustering results file. This also means that you should wait for a result to finish processing before downloading the batch 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. Optionally enter a name for your batch download – this will be the name of the .zip file

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

  4. Results are automatically exported on a .zip file



We are so excited to share these new additions to CODI Beta that will help you be more productive with your research. Let us know what you think!


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