How to guide: Creating an EV or LNP Report

How to guide: Creating an EV or LNP Report


The EV or LNP Report can be generated at any time in CODI using the “cross dataset report” feature, which provides a report for a single chip with up to 4 lanes.

To generate a report, navigate to the CODI collaboration in which the data is saved and perform the following:
  1. Click the Analysis Results button to view all the analysis result in this collaboration
  2. Click on the “Cross Dataset Report” button 
  3. Select the analysis app and settings to filter the results list. Note: all datasets in a single report must be batch analyzed with the same analysis settings to be included in the report.
  4. Select the datasets from one chip (one dataset corresponds to one FOV) to be featured in the report and click “Generate Report”. 

InfoThe EV batch report is for a single chip and up to 4 lanes, i.e., it is not possible to generate a single analysis report for datasets acquired from different chips, or analyzed with different analysis settings.
To generate cross-chips reports, ONI provides EVP2 axis, an offline python-based code tool.
For more information on the EVP2 axis, visit the ONI EVP2 axis webpage. 
Info
Key Tip: Report generation only works for data generated from AutoEV, which contains the proper key/value tags to ensure that the report is calculated and displayed correctly.
If an error message appears during the report generation process, it is likely because the datasets do not contain the proper tags, such as the “Lane” and “FOV” Key/Value tags.
Alert
The report's layout may change depending on the resolution of the screen being used to generate the report. If the contents or plots look incorrect, try maximizing the browser window. If there continue to be issues (when using a smaller laptop screen, for example), try using the Nanoimager laptop or Aplo Scope desktop PC to generate the report.

EV Report

The EV Report template is used when a batch report is generated from analyses from the following analysis apps:
  1. EV Profiling
  2. AI EV Profiling
The EV Report provides an overview of key information about the count, size, and biomarker positivity of the selected datasets. The data is presented in a familiar 4-column format with a column representing the data from a lane of the ONI 4-Lane Assay chip, making it easy to compare information across samples.



Experiment Summary

The left-most column of the report contains key information used to generate the report:
  1. Analysis App
  2. Analysis Settings
  3. Date Generated
  4. User name of CODI account
  5. Positivity
    1. Counting thresholds for positivity
    2. Localization or Bins counting
  6. Size
    1. Description of which localizations were used when calculating the size.

Lane and Channel information

The header of each lane displays the primary information about the sample:
  1. Lane Title, which is generally recommended to be the name of the sample
  2. Channel names for the acquired channels, which are typically the biomarker or staining
Idea
Notice that the channel colors are consistent from autoEV, through CODI's analysis interface and into the report, helping create a mental map between each channel and its associated staining

EV Count 

The EV count for each FOV is displayed. Quickly comparing in a single lane can help assess sample homogeneity, and across lanes to compare the number of EVs in different samples.

Positivity

Biomarkers positivity aggregated across the FOVs in each lane is represented as a stacked bar chart to easily compare across lanes. Positivity is displayed as a percent and as an absolute EV count.

EV Size (Diameter)

EV size for each positivity class is displayed as a box plot, allowing for easy comparison across positivity classes and across lanes. The overall EV size (gray distribution) is displayed as an aggregate of all positivity classes.

EV size is calculated as shown below, by using the convex hull area of the cluster ("Area (nm^2)" in the results CSV) and calculating the diameter of a circle with the same area.

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