pyme-omero

This is a PYME plugin which enables interoperability between PYME and an OMERO server. Contributions / feature requests welcome.

Current Features / how-to

• Load localizations attached to an OMERO image in PYMEVis
  1. Open PYMEVis
  2. Clicking File > Open OMERO
  3. copy the OMERO Link to this image into the dialog box.
  4. Click OK.
• Upload localizations from PYMEVis to OMERO server attached to a snapshot of the current view
  1. Open localizations in PYMEVis, and set the view how you like
  2. Click File > Save to OMERO > Snapshot.
  3. Enter the project and dataset the image should be uploaded/linked to. The project/dataset will be created if they don't already exist.
  4. Click OK. The current pipeline datasource localizations as well as the upstream Localizations datasource (if present) will be attached to the thumbnail on OMERO.
• Upload localizations from PYMEVis to OMERO server attached to a PNG/TIF rendering
  1. Open localizations in PYMEVis
  2. Click File > Save to OMERO > PNG or File > Save to OMERO > OME Tif.
  3. Select your rendering method/settings and enter the OMERO project/dataset names the image should be uploaded/linked to. The project/dataset will be created if they don't already exist.
  4. In the Input Localization Attachments table, click to open the table menu and add a localization attachment. You can attach multiple localization sets from the recipe to the image. Their filenames will be whatever you enter in the Table Name box, defaulting to an .hdf extension if you do not specify one.
  5. Click OK.
• Load image from an OMERO server in dh5view
  1. From an open dh5view window, click Modules > omero_io.
  2. Click OMERO > Open,
  3. Copy the Link to this image from e.g. OMERO.web into the text box
  4. Click OK.
• Upload image from dh5view window to an OMERO server
  1. From an open dh5view window, click Modules > omero_io.
  2. Click OMERO > Save to OMERO.
  3. Enter the project name (optional) and dataset name the image should be uploaded/linnked to. The project/dataset will be created if they don't already exist.
  4. Click OK.
• Upload images/localizations from a recipe run on a PYME cluster or in the PYME bakeshop
  1. create a recipe using any of the upload modules in the omero_upload section of the Add Module menu in the recipe GUI.

Installation

1. install PYME
2. install omero-py
3. clone this repository

   git clone https://github.com/python-microscopy/pyme-omero
   

4. run

   python pyme-omero/setup.py develop
   

   • Note - mac users installing to conda environments will need to run setup.py using a 'framework build', accomplished by running

     /opt/miniconda3/envs/myenv/python.app/Contents/MacOS/python pyme-omero/setup.py develop
     

     or similar depending on your conda install location.
5. In the GUI dialog, enter your OMERO server information/credentials, which will be stored in the PYME config directory (typically .PYME folder in your user directory).

Manual configuration

You can manually edit the configuration file, .PYME/plugins/config/pyme-omero which should contain the OMERO server information in yaml format, e.g.

user: <your OMERO user name>
password: <your OMERO password>
address: <OMERO server IP address>
port: <OMERO server port>

noting that port is optional if your OMERO server uses the default port (4064).