Open Microscopy Environment

Hello,

I want to use mtools for the first time to measure intensities. However, when I click “choose datasets” the dataset chooser windows opens but closes immediately again. And I can’t do anything about it.
The same problem also occurs with “Measure Spots”, “Event timer” and “FRAP” but not with the other applications. Only when I click “Distance Measure” the whole mtools shuts down.

It really seems to be a “choose datasets” problem.

Interestingly, I have the exact same problem on a Mac and a Windows 7 PC.

I am using OMERO.mtools 1.1.0 and uploaded the images with OMERO.insight

Thanks for the help

Hi Jan

I'm sorry you've been having these problems using mtools. To accurately link results to original images, and to help with navigating data, mtools expects a strict Project -> Dataset -> Images hierarchy. This allows for quite convenient batch processing of images, dataset at a time. From your description I suspect that your images do not follow this hierarchy and are either not imported into datasets, or that your datasets are not in projects.

You can see in insight how your data has been imported, using the Projects tree in the left hand panel.

If this does not help with your problem by all means please get back in touch so we can hopefully find a solution.

I have been working lately on mtools giving some feedback when this situation is encountered, and a new version can be released soon.

Again, sorry for this problem.

Michael.

Hi Michael,

Thank you for your reply.

Unfortunately, this didn't solve the problem. I had my images organised like: Project -> Dataset -> Images

I also deleted everything, created the folder first and then uploaded the images again, but this didn’t help.

However, the first image that I ever uploaded with OMERO.insight was not organised in the hierarchy like above and was located in the folder “Orphaned Images”.
This folder is still there and I can’t delete it.
Could this maybe cause the problem?

Thanks for your help!
Jan

Hi Jan

Not at all, I should have created some user docs to help people out! mtools originated as a set of tools for people in the labs around me, so I was always there to speak to them. As more features have been added to the suite it became a much more daunting task to detail the workflows, but there is no real excuse for me not doing it.

Firstly, the orphaned images 'folder' is a permanent feature to house any images that you choose not to belong to a project or dataset. mtools cannot access this but it is certainly not a problem.

Depending on the version of mtools you have, you might have a log file located at C:\Users\username\omero\mtoolsLog.txt. If this file exists can you please upload it as an attachment here?

So, briefly, the intensity analysis tool is aimed at batch analysis at the dataset level. It will only analyse images that contain rectangular ROIs (e.g. around a cell) in 2D or 3D. These can be drawn in OMERO.insight.

Enter your username/password etc and click the 'Intensity Measure' button. This will log you in and you are asked to choose your group. It is very important to check which group you imported your images into, as you can only see data in the group that you log in to.

At the ImageSegmentation window, from the File menu select 'Choose datasets' (as you have been doing). When you select a project the datasets it contains should be listed in the left-hand panel. Select each one you want to analyse and click the '+' button to add it to the right-hand panel. At the moment multi-select is not possible, but this will change.

When you click 'ok' the images in those datasets that do not contain ROIs are filtered out. The remaining images are then available from the 'Select Images' pull-down box so you can test your segmentation on multiple images. I recommend playing with the controls on this window to see what happens - a preview of your segmentation will be visible in the right-hand image window.

When you are happy with the setting you can click 'ok' to process each image in turn, and when this is finished you will be asked where to save your data as .xls (Windows) or .csv (Mac).

If none of this is helpful then I will find a way tomorrow to get you what you need.

Best,

Michael.

Thanks a lot for the detailed explanation!

I was looking for the log file, but even on my windows 7 PC there isn’t this file. This probably doesn’t make the whole thing easier.

The images contain rectangular ROIs, but unfortunately this doesn’t help. I can’t go further than to the point “Choose datasets“ since the window closes immediately.

I will upload another set of images tomorrow, to exclude that this is the problem.


Thanks again!!

Jan

As a notice to the community:

Jan kindly tested the forthcoming 1.2.0 version of mtools and this fixed the problem. This version should be available to download from the Partner Projects area of the openmicroscopy website in the next few weeks after we subject it to some more testing.

Many thanks to Jan for feedback and patience.

Michael.