simple-omero-client

A Maven project to easily connect to OMERO.

This library presents a simplified API to put/get objects on an OMERO server.

It can be used from Maven.

The JAR can be put into the ImageJ plugins folder to use it from scripts.

How to use

Connection

The main entry point is the Client class, which can be used to retrieve, save or delete objects.

To use it, a connection has to be established first:

Client client = new Client();
client.connect("host", 4064, "username", password, groupId);

Repository objects (projects, datasets, images, screens, wells, plates)

It can then be used to retrieve all the repository objects the user has access to, like projects or datasets:

List<ProjectWrapper> projects = client.getProjects();
List<DatasetWrapper> datasets = client.getDatasets();

These objects can then be used to retrieve their children:

for (DatasetWrapper dataset : datasets) {
    List<ImageWrapper> images = dataset.getImages(client);
    //...
}

Annotations

For each type of objects (project, dataset or image), annotations can be retrieved/added, such as:

• Tags:

TagAnnotationWrapper tag = new TagAnnotationWrapper(client, "name", "description");
dataset.link(client, tag);
List<TagAnnotationWrapper> tags = dataset.getTags(client);

• Key/Value pairs:

dataset.addPairKeyValue(client, "key", "value");
String value = dataset.getValue(client, "key");

• Tables:

TableWrapper table = new TableWrapper(columnCount, "name");
dataset.addTable(client, table);
List<TableWrapper> tables = dataset.getTables(client);

• Files:

File file = new File("file.csv");
dataset.addFile(client, file);

Images

Pixel intensities can be downloaded from images to a Java array or as an ImagePlus:

double[][][][][] pixels = image.getPixels().getAllPixels(client);
ImagePlus imp = image.toImagePlus(client);

Thumbnails of the specified size can be retrieved:

int size = 128;
BufferedImage thumbnail = image.getThumbnail(client, size);

ROIs

ROIs can be added to images or retrieved from them:

ROIWrapper roi = new ROIWrapper();
roi.addShape(new RectangleWrapper(0, 0, 5, 5));
roi.setImage(image);
image.saveROIs(client, roi);
List<ROIWrapper> rois = image.getROIs(client);

They can also be converted from or to ImageJ Rois:

// The property argument is the name of the ImageJ property used to create 3D/4D ROIs in OMERO, 
// by grouping shapes sharing the same value (e.g. label/index).
// The ROI name can be set/accessed using the property ROI.ijNameProperty(property).
// The OMERO IDs are available through the property ROI.ijIDProperty(property).
// The ijNameProperty() and ijIDProperty() methods append "_NAME" and "_ID" to the property (respectively).
// By default, the property is "ROI", and thus, the name property is "ROI_NAME" and the ID property, "ROI_ID".
ROIWrapper roi = new ROIWrapper();
roi.setName("ROI name");
roi.addShape(new RectangleWrapper(0, 0, 5, 5));
List<Roi> imagejRois = roi.toImageJ();
String name = imagejRois.get(0).getProperty(ROIWrapper.ijNameProperty(property));
String id = imagejRois.get(0).getProperty(ROIWrapper.ijIDProperty(property));

// Conversely ImageJ Rois can be converted to OMERO from ImageJ using "ROIWrapper::fromImageJ"
Roi ijRoi1 = new Roi(1.0, 2.0, 3.0, 4.0);
ijRoi1.setProperty(property, 0);
ijRoi1.setProperty(ROIWrapper.ijNameProperty(property), "Name 1");
Roi ijRoi2 = new Roi(2.0, 3.0, 4.0, 5.0);
ijRoi2.setProperty(property, 1);
ijRoi2.setProperty(ROIWrapper.ijNameProperty(property), "Name 2");
List<Roi> ijRois = new ArrayList(2);
ijRois.add(ijRoi1);
ijRois.add(ijRoi2);
List<ROIWrapper> rois = ROIWrapper.fromImageJ(ijRois);

About Tables & ROIs

An OMERO Table can be created from an ImageJ ResultsTable. Rows can also be linked (optionally) to ROIs on OMERO by having a column identifying the ROIs and passing ImageJ ROIs as an argument:

TableWrapper table = new TableWrapper(client, resultsTable, imageId, ijRois, property);

Each row will have the image ID in a column named "Image", and the ROI IDs in a "ROI" column. However, for ROIs to be linked, several conditions have to be fulfilled:

1. ImageJ ROIs should have an ID property set containing the ROI ID on OMERO (property + "_ID"). Saving the local ImageJ ROIs and converting back the OMERO ROIs to ImageJ can be done to accomplish this.
2. The ResultsTable should have a column to identify the ROIs, which can be done in several ways:
   1. A column can be named with property + "_ID" and should contain the OMERO IDs.
   2. Or it can be named property and should contain either:
      1. The ROI local index.
      2. The ROI ID on OMERO.
      3. The name of the ROI.
      4. The name of a shape from the ROI.
   3. Alternatively, it can be linked if the Label column of the ResultsTable contains:
      1. The ROI name.
      2. The name of a shape from the ROI.

Rows can be added the same way to the table:

table.addRows(client, resultsTable2, imageId2, ijRois2, property);

License

GPLv2+