Extending J-AST (JIPipe plugins)

J-AST comes with a plugin interface that facilitates the easy addition of new operations.

A plugin comprises of a JIPipe 5.3.0 *.jip project that is being copied into the share/plugins directory. The application/server needs to be restarted to recognize the plugin.

The JIPipe project must adhere to specific constraints, so it is an effective plugin:

The project must have a project-wide directory with the key tmp_dir. This key is automatically set by J-AST and will point to the directory that contains all inputs and outputs
The name and description of the project must be set. The information will be used inside the J-AST frontend.
Parameter references should be avoided if possible. Instead, use project-wide parameters. JIPipe 5.3.0 projects lack easy methods to recover parameter types, thus the backend will be left with guessing the correct type.
The project must have a specific set of project-wide parameters that contain information for J-AST. The parameters are described below.

J-AST metadata parameters

Create the following project-wide parameters. J-AST will use the information contained within them to create the associated backend workload.

Type	Key	Description	Allowed values
Boolean	`jast_plugin`	Must be true for J-AST to recognize the plugin	true/false
String	`jast_plugin_category`	The menu category where the operation will be placed	Can be empty
String	`jast_plugin_assay_type_restriction`	Allows to restrict the operation to a specific assay type	DDA/ETest/Unknown. Can be left empty (no restriction). Defaults to empty.
String	`jast_plugin_mode`	Determines how images are related to each other (each processed by itself, alway process whole timeline row/column)	Single/FullRow/FullColumn. Defaults to Single.
String	`jast_plugin_view_mode_restriction`	Allows to hide the operation from certain project modes	Timeline/Grid. Can be left empty (no restriction). Defaults to empty.
Boolean	`jast_plugin_generates_results`	Must be checked if results should be extracted by J-AST	true/false
String List	`jast_plugin_inputs`	List of inputs that will be available in the temporary directory	plate/strip/disk/strip-disk/zoi-shape
String List	`jast_plugin_outputs`	Lists of outputs that will be generated in the temporary directory	raw/plate/strip/disk/strip-disk/zoi-shape/pixelSize

Inputs received from J-AST

You will need to prepare your pipeline to handle the folder structure that J-AST produces as pipeline inputs. The pipeline receives inputs in form of files/directories located in a temporary directory, which is passed to the pipeline through the tmp_dir directory.

metadata.csv

This file contains all text metadata for each image. The file is structured as following:

#ImageId	#Experiment	#Sample	#TimePoint	#AssayType	PixelSize	GroupRow	GroupColumn
...	...	...	...	...	...	...	...

Raw images

A directory raw is always created and contains the raw image files named according to their unique database ID (#ImageId).

Mask annotations (ROIs)

Mask annotations (0 = background, 255 = foreground) are placed in directories named after the unique annotation ID and named according to the related image ID.

The currently supported mask annotation Ids are:

plate: the plate mask
strip-disk: the E-Test strip or DDA disk (depending on assay type)
zoi-shape: the E-Test ZOI shape (black for DDAs)

Expected outputs

All outputs must be written relative to the tmp_path path and follow rules based on the output type.

Modified raw images

J-AST will read modified raw images from a directory raw_updated. The contained images must be PNG files named after the #ImageId.

Mask annotations

J-AST will read mask annotations from a directory named according to the mask annotation ID. The contained images must be PNG files named after the #ImageId. The masks must have the same size as the raw images.

Results

Arbitrary results must be written into a directory results. If jast_plugin_generates_results is true, J-AST will automatically explore the directory and copy all files into its internal filesystem.

02 December 2025