Download and export images ========================== We will show the possibilities of getting images from OMERO. These can be described as "export" (new image, usually a jpeg, tiff or png is created from the original image saved in OMERO) or "download" (the original image, in the original format is downloaded from OMERO). **Description** --------------- Image export and download can be achieved using any of the three main clients for OMERO: OMERO.insight, OMERO.web or the Command Line Interface. Further, we have developed an "omero-downloader", a command-line application dedicated specifically to the downloading and exporting of images and annotations from OMERO. We will show: - How to export images from OMERO.web - How to download images from OMERO.web - How to use "Batch image export" script for batch exports of images - How to use OMERO.downloader for downloads and exports - How to use OMERO.downloader for export of metadata associated with the images - How to navigate through the structure created by OMERO.downloader **Setup** --------- - omero-downloader was installed by downloading and unzipping of the `release artifact `_. - omero-downloader works on Mac, Windows and Linux. **Resources** ------------- The documentation on OMERO.downloader can be found at https://github.com/ome/omero-downloader/blob/master/README.md Downloader commands used in this walkthrough are in https://raw.githubusercontent.com/ome/training-scripts/master/practical/bash/downloader-commands **Step-by-Step** ---------------- #. In OMERO.web, select one or more images you want to download. Then, find in the top of the right-hand pane the download icon |image1|, click on it and select the desired action, for example Download, which downloads the data in original format. #. Open the downloaded file(s) in the software of your choice. #. To export images in a different format such as PNG, TIFF or OME-TIFF, we can use a script on the server to build a zip for download. Select images, click on the script icon |image2| and click on “export scripts” and then choose "\ Batch Image Export...\ ". You can choose to export individual channels and/or the "merged" image (current rendering settings). It is also possible to export multiple Z and T sections. The image Format can also be specified. If OME-TIFF is chosen, the Channels and Z/T sections are ignored and the entire image is exported as an OME-TIFF image. #. Click ``Run Script`` to generate the zip on the server. When the script completes, the Activities panel will display the result. #. Click the ``Download`` button to download the zip .. image:: images/download3.png #. Open one image in OMERO.iviewer and draw several ROIs. Back in webclient, add several Tags onto the same image. Using the download icon in the right-hand pane, |image1| export the image as OME-TIFF. #. Reimport the OME-TIFF again into OMERO and verify the imported image still has the ROIs and Tags, same as the original image prior to export. Note: This workflow can be used to transfer the image with its metadata into another OMERO.server if available. Image export using omero-downloader (demo only) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #. Open a CLI terminal on your machine and go into the directory where omero-downloader is installed. #. To download a single image, run the following command. It assumes that the target directory already exists e.g. /tmp/repo - On Mac or Linux Copy the following command from \ https://raw.githubusercontent.com/ome/training-scripts/master/practical/bash/downloader-commands :: $ ./download.sh -b /tmp/repo -s -u -w -f binary Image: - On Windows Copy the following command from \ https://raw.githubusercontent.com/ome/training-scripts/master/practical/bash/downloader-commands :: $ download.bat -b /tmp/repo -s -u -w -f binary Image: #. To download all images in a Dataset, run - Copy the following command from \ https://raw.githubusercontent.com/ome/training-scripts/master/practical/bash/downloader-commands\ into your Terminal. :: $ ./download.sh -b /tmp/repo -s -u -w -f binary Dataset: - Note that you will be able to deduce what tags and annotations the downloaded images were annotated with. - Go to OMERO.web and Tag several images from two datasets with a tag "your-name". Then, go back to the command line and run - Copy the following command from \ https://raw.githubusercontent.com/ome/training-scripts/master/practical/bash/downloader-commands\ into your Terminal. :: $ ./download.sh -b /tmp/repo -s -u -w -f ome-xml Dataset:$ID2,$ID1 This will download the xml metadata for images in those two datasets (Note: we could download all the images as well, but we can do it at any later point, as downloader "remembers" what is downloaded already and does not re-download it twice.) - Copy the grep command from \ https://raw.githubusercontent.com/ome/training-scripts/master/practical/bash/downloader-commands\ into your Terminal. - This will find the IDs of all the images from the two datasets tagged with "your-name" tag. .. |image1| image:: images/download1.png :width: 0.25in :height: 0.26042in .. |image2| image:: images/download2.png :width: 0.4375in :height: 0.35417in .. |image3| image:: images/download3.png :width: 3.78646in :height: 1.22804in