Open Microscopy Environment

Hi, iam using the Omero Insight 4.1 version, and sadly, the Export functionality does not work now as expected.
In 4.0, the image is exported nicely, under the My Documents folder, with a single click.

But now, iam asked a folder to choose, and when i selected desktop, the download process started, took a long time, and finally i saw a file with a name "null" on the desktop. When i opened it, with Microsoft Picture Manager, i saw a collection of images inside it, which are actually on my desktop.

Please suggest, how to make this functionality work, else i think it is better to revert back to the 4.0 version export functionality.

Hi Ryan,

In 4.1 the image export is exporting the image as an ome.tif. This includes all the planes of the image, as well as a limited amount of the image metadata in the OMERO database. This is why it takes some time to export. To view all of this, you can open the image in ImageJ, using the BioFormats plugin, available as "loci_tools.jar" here http://www.loci.wisc.edu/ome/formats-download.html

There is a small bug in the naming of the exported file: The image name is cleared when you select a new directory, so you have to enter the image name again before saving.

Thanks for your interest,

Will.

Hi, thanks for the reply. I see that when we click on the "Download the Archived File" button, the download does not happen.

When i selected an archived image, and clicked on "Download" button, in the file chooser dialog, the desktop is selected, and in the File Name box, it is written as: C:\Documents and Settings\ryan\Desktop .
I have added a "\" at the right, and then added test.tif

But when i clicked on Download, nothing happened.

Hi Ryan,

I just tried this with an .oib image in the latest revision of Insight and server and it worked OK. Are you using a recent revision of Insight? This should be working in the released version.
We had a bug recently where the downloading progress window did not show in front of the main window, so maybe that's the problem?
We've just reproduced the "null" image name bug you mentioned in the first post, so we'll try and get that fixed too.

Will.

Hi, i would like to export the entire project and dataset with images in them, when i click on Export button.
I mean, i want to store all the hierarchy of the project, dataset and images, when i export them.

For ex., if i select a project, and click on Export, i want to export all the images in the datasets of the project, with a hierarchy.

For this, can i write a query to fetch the data and the entire hierarchy, and save them in the system?
If it is possible, please advice. Waiting for the replies.

We have already all the methods in place to retrieve all the images within a dataset.
so nothing stop you then from export all the images.
We do not have the method yet in the server allowing to select a dataset and export all the images within that dataset.

Cant we get the images by writing a custom select query in the OmeroGateway.java, such that i can specify the dataset id or project id, to retrieve all the images?

ryan wrote:Cant we get the images by writing a custom select query in the OmeroGateway.java, such that i can specify the dataset id or project id, to retrieve all the images?

Sure. Or you could use the existing queries that do just that as part of IPojos.

Thanks for the reply, Can you please give any example of a query showing how to retrieve all the images based on the project id, or dataset id ?
I want to download all these images into my system.

You can use the IContainer service.
Do retrieve all the Datasets/Images within a project, you can do.

Code: Select all

ParametersI param = new ParametersI();
param.exp(omero.rtypes.rlong(userID)); //not require if project id is specified
param.leaves(); //to get the images
List projectIDS;
IContainerPrx service;
service.loadContainerHierarchy(Project.class.getName(), projectIDs, param);




This call will return the Project with all the datasets and all the images within the datasets

To retrieve the images within a dataset only.

Code: Select all

service.loadContainerHierarchy(Dataset.class.getName(), datasetIDs, param);