Analyzing images
Once your images are prepared — with metadata, plate annotations, disk/strip annotations, and (for E-Tests) ZOI shape annotations — you can run analysis operations to extract quantitative results.
DiskImageR-style analysis (RAD/FoG/ZOI)
This analysis is based on the DiskImageR method (Gerstein et al.) and computes drug resistance metrics from your annotated images.
- RAD (Radius of Inhibition)
The radius at which colony growth is reduced by a given percentage threshold (default: 20%, 50%, 80%).
- FoG (Field of Growth)
A metric that quantifies the overall growth across the zone of inhibition, calculated across time points.
- ZOI (Zone of Inhibition)
The boundary of the zone where no growth is observed.
Two variants are available:
DiskImageR-style analysis (RAD/FoG/ZOI) - Single images: Processes each image independently. Available for both timeline and single-image projects.
DiskImageR-style analysis (RAD/FoG/ZOI) - Timeline only: Processes entire timeline rows at once, enabling FoG calculation across time points. Requires the timeline view mode.
The algorithm works by generating label areas around the strip/disk following the ZOI shape, then finding for each percentage threshold the label with the corresponding brightness reduction to determine the RAD. For timeline analysis, the ZOI is applied to other time points to calculate the FoG.
Select the images to analyze.
In the tab, choose the appropriate DiskImageR analysis variant.
Configure the parameters (thresholds, etc.) and click .
Once the task completes, view the results via the button. See Viewing results.
Auto-detect MIC (E-Test only)
This operation automatically determines the Minimum Inhibitory Concentration (MIC) for E-Test images. It applies OCR (optical character recognition) to align the strip ticks to the reference concentration sequence from the strip preset, then captures the average colony intensity per concentration to determine the MIC.
- Requirements
The image must be annotated as E-Test assay type
The strip annotation must be present
The ZOI shape annotation must be present
A strip preset must be assigned to the image
The pixel size must be calibrated
The server must have Tesseract OCR and R installed (desktop app includes these)
- Output
The detected MIC value is written back to the image's MIC metadata field. The operation also generates result files with detailed analysis data.
Key parameters include:
- MIC threshold
The intensity threshold used to determine growth versus no growth.
- Confidence threshold
Minimum OCR confidence required for tick recognition.
- Target DPI
The resolution at which OCR is performed.
- Corridor widths
Width of the intensity sampling corridor along the strip.
Generating visualizations
J-AST can generate overlay visualizations that show the detected annotations (plate, strip/disk, ZOI shape) on top of the raw images. These are useful for quality control and for presentation purposes.
Generate visualizations (single): Creates a visualization for each selected image independently.
Generate visualizations (time series): Creates visualizations that require images organized into time series (timeline view mode).
Visualizations are stored as results and can be viewed and downloaded via the results browser.
Export for custom pipelines
If you have created custom JIPipe plugins or want to process your data outside of J-AST, the Export for custom pipelines operation exports the selected images with all annotations and metadata into the results directory for download.