All-in-one preparation

J-AST provides an All-in-one preparation operation that automates the entire preparation pipeline in a single step. Instead of running metadata extraction, timeline sorting, plate detection, disk/strip detection, and ZOI shape detection individually, you can let J-AST handle all of them at once.

Running the operation

Select the images you want to prepare. You can use SELECT ALL or SELECT ALL UNSORTED to select multiple images at once.
In the right-hand properties panel, switch to the Process tab.
Search for All-in-one preparation in the operation tree and click it.
Configure the parameters (see below) and click OK to start.

Parameters

The operation provides toggles to enable or disable individual steps, allowing you to skip parts that are already done or not needed:

Fill metadata: If enabled, runs the auto-fill metadata step using the provided delimiters and field configuration.
Sort images into timeline: If enabled, runs the auto-sort by metadata step. Requires the time point order to be specified.
Find plate: If enabled, runs automated plate detection and pixel size calibration.
Find DDA disk / E-Test strip: If enabled, runs the appropriate detection algorithm based on the assay type (DDA disk v3 for DDAs, E-Test strip v1 for E-Tests).
Find E-Test ZOI shape: If enabled (E-Test only), runs the ZOI shape detection and registers the ZOI shape across the timeline.

You will also need to provide:

Time point order: The ordered list of time points as detected in your metadata. Click the input field and add time points in the correct chronological order.
DDA / E-Test keywords: Keywords used to distinguish DDA from E-Test images during metadata extraction (e.g., dda and etest).
Default assay type: The assay type to assign to images that do not match any keyword.
Filename delimiters: Characters used to split the file name into metadata components (default: _-).
Plate diameter (mm): The physical diameter of the plate, used for pixel size calibration.
Expected disk diameter (mm): The expected DDA disk diameter, used by the disk detection algorithm.

What happens behind the scenes

The operation runs the following pipeline for each selected image:

Extract metadata from file names (if enabled)
Sort images into timelines (if enabled)
Detect the plate and calibrate pixel size (if enabled)
Detect the DDA disk or E-Test strip (if enabled)
Detect the E-Test ZOI shape and register it across the timeline (if enabled, E-Test only)

13 July 2026