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Download IDR/OMERO (version 0.45)

Which OMERO instance to connect?:

By default, the tool will download a tarball containing individual images from IDR into your Galaxy history. If you need to connect to your own instance, set your connection username and password from User->Preference->Manage Information

How would you like to specify the IDs of images to download?:

Image IDs to download:

You can enter a single image-id, or a comma (or '|')-separated list of IDs. Alternatively, you can paste here a link to an image selection obtained through the IDR webclient.

Which images do you want to download?:

Name of the channel to download:

For all image IDs only the specified channel will be downloaded. If left empty, the first channel (whatever this is) will be downloaded by default.

z-plane of images to download:

Image frame to download:

Limit the download to a selected region of the image?:

Skip failed retrievals?:

By default the tool will fail with an error on the first non-retrievable image ID. Here, you can choose to skip non-retrievable image IDs and continue downloading the available ones instead. The error log will contain warnings about failed IDs in this case.

Download images in a tarball?:

By default, the tool will download a tarball containing individual images into your Galaxy history. This option is strongly recommended, especially for a large number of files. With this option set to No, you will download a collection of images, only suggested for a small number of files.

Download image data from the IDR (Image Data Resource) - a public repository of reference image datasets from published scientific studies.

Input

A set of image IDs as can be obtained from the IDR webclient like this:

Select the wells you want to download in the thumbnails.
Select at the bottom the images in those wells that you want to download (one well might contain several images).
Click on the 'Link' button on the top right of the page and copy the provided URL.
Paste the URL into the input field of this tool, for example:

https://idr.openmicroscopy.org/webclient/?show=image-9036708|image-9036710|image-9036711

Alternatively, you can simply provide a list of known image IDs in the text input field (comma or '|'-separated ), or as an input file (each ID on a separate line).

Finally, if you want to download all images of a single dataset. Specify the id as All images from a single Dataset ID.

Most images in the IDR have more than two dimensions. Thus, there are parameters available which allow you to select a particular recording channel, z-plane or time frame to download. You can also select a region which will be used to crop the images, rather than downloading the entire file.

Output

Downloaded images will be saved in TIFF format. If you selected multiple image IDs to download, these will be saved as elements of a collection.

The accompanying error log dataset may hold valuable information about requests that could not be fulfilled exactly as specified, or that were found to be ambiguous.