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OMERO Reader (5.2)

OmeroConnector-Node extension for KNIME Workbench version 0.11.0.v202006260943

This (experimental) reader uses OMEREO.insight to access images from OMERO databases. In the configuration phase the insight viewer is used as graphical interface to select image IDs from the database. During the node execution the images are loaded from the database and get converted into an appropriate ImgLib format.

Options

user credentials

Server
The address of the OMERO server.
Port
A port that can be used to connect with OMERO.insight to the server (default value 4064).
Connection
The speed of your server connection LAN, High (Broadband) or Low (Dial-up)
Username
The username, that you use to access the server with OMERO.insight
Password
The password, that you use to access the server with OMERO.insight
Encrypted Connection
If the connection to the server is encrypted, this equivalent to the closed padlock setting in OMERO.insight or OMERO.web.

image selection

Selection
  • Fill in the user credentials form.
  • Start OMERO.insight by clicking onto the start button.
  • Browse the database and select images with your mouse.
  • Right click on one/multiple selected images to access the context menu.
  • Select "View->View in KNIME" to transmit the image ID
  • Repeat this for all images that should be loaded to your workflow
  • Close OMERO.insight. The image IDs are listed in the IDs field and the node is ready for execution.

Output Ports

Icon
The images that have been loaded from the OMERO database

Views

Table Cell View
Shows the loaded images in a table cell view

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install KNIME Image Processing - OMERO Integration from the following update site:

KNIME 4.2

A zipped version of the software site can be downloaded here.

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Developers

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