Generating Reports
After your WSIs are processed by the QC service, you can easily visualize the computed masks using reports created by the Reporting Library. By default, the masks are overlaid using cyan color and only per-pixel masks are shown (you can manually toggle the per-tile masks).
🌐 Service Address
The report can be created by sending a PUT request to the following endpoint:
http://rayservice-qc-serve-svc.rationai-jobs-ns.svc.cluster.local:8000/report
🧬 Structure of the PUT Request
🔒 Required Parameters
The request body must include:
| Parameter | Type | Description |
|---|---|---|
backgrounds |
list[string] | List of paths to the processed WSIs. All of the WSIs must be located in a single directory. |
mask_dir |
string | Path to the directory where the computed masks are stored. |
save_location |
string | Location where the report will be saved, including the name of the file (e.g., "/mnt/data/thrash-bin/report.html"). |
🎛️ Optional Parameters
Optionally, you can include the following parameters:
| Parameter Name | Type | Default Value | Description |
|---|---|---|---|
compute_metrics |
bool | True |
Toggles if the generated report should contain aggregated metrics about the slide's coverage by the different classes of artifacts. |
📊 Aggregated Coverage Metrics
When the compute_metrics optional parameter is set to True, the generated report will include aggregated coverage metrics computed for each slide.
These metrics aggregate artifact coverage by a certain class of artifacts across all of the WSI's processed tiles.
Currently, the mean and median coverages are computed.
Additionaly, tiles with fewer than 5% of pixels examined by a given QC function are excluded from the aggregation.
The following image showcases a sample slide in a report with computed aggregated coverage:
Existence of the Coverage Metrics
Please note that in order to succesfully include the coverages into the report, the values must be computed and stored by the QC service. This is now done automatically, but it was not the case for the previous versions of the service.
Tip
The aggregated metrics for a given WSI are stored in a CSV file in the same directory as the QC masks.
The file naming convention is <slide_name>.csv.