Open Microscopy Environment

Some acquisition software allow the user to create events during the experiment, or even after the experiment. This is simply a tag on a specific frame. I found one vague reference in the OME description (http://www.openmicroscopy.org/site/supp ... ight=event) stating that this data was in the OME-XML file, but I can find no documentation. I am trying to convert other files with markers into OME tiffs, but I need the Event Marker data. Any and all help would be appreciated.

Hello,

Events like laser ablation would be recorded as a MicrobeamManipulation, these are stored at the Image level and link to a ROI to define the area they affect. The also optionally contain links to any light sources that were used for the operation.

The stage motion is recorded directly on the Plane using the PositionX, PositionY, PositionZ attributes.

You can also store an explicit StageLabel on an Image. This is a Name with an x,y,z position in stage coordinates.

Hope theses links are useful, let me know if you have any other questions.

Cheers,

Andrew

Thanks Andrew, that is helpful, but I am looking for something different. In Nikon Elements, Metamorph and Andor iQ software it is possible to set it up to mark a frame as an event frame upon receipt of a TTL from an external source. The most common is probably a TTL from Patch-clamp device, but I've seen it from syringe pumps, lasers, microfluidic pumps and just the user tapping the keyboard. So I know this information is saved in the Meta-data, but it does not seem to get transferred when I save as an OME-TIFF.

Hi,

Thanks for the further info. I am not sure how this data would fit at the moment. It would be really helpful if you could send us some sample files from Nikon Elements, Metamorph and Andor iQ that have these type of events stored in them.

You can use the QA system to send files to us:
http://qa.openmicroscopy.org.uk/qa/upload/

We can have a look at them and suggest the best place for the data.

Ta,

Andrew

Hi Andrew, I uploaded two files: one Andor Tiff (EventTest) and a Nikon nd2 (Particles_Event19_40). Both have a user created event that stays with the file. Thanks for your help.

Thanks, we will have a look at them and I will create a ticket for the work.

Andrew

Sorry to resurrect a dead thread. I am new to OME, but have the same problem: I am sending multiple TTLs to a Nikon microscope, and these are recorded in the .nd2 file. They correspond to start and endpoints of presented movies. I can see their timings with NIS Elements Viewer, but am not sure how to access them in MATLAB. I uploaded [to OME QA] a file (16_8_16_TTLtest1003.nd2), which is a timeseries directly recording the luminance of a screen, so I can see/correct for latencies between TTLs and movie presentation. Any help would be much appreciated.

Andrew

Hi Andrew,

thanks for your question and uploading the sample file. In the general case, I would expect the format metadata to be stored and accessible via the original metadata, i.e. as key/value pairs that can be retrieved using the Bio-Formats MATLAB interface.

In the case of the Nikon ND2 format and this type of metadata, it looks like the individual events displayed in the NIS Elements Viewer are not parsed by the Bio-Formats reader and are not available via the original metadata. I can create a ticket to request support for this type of metadata and have you cc'ed on the ticket to get updates if you are interested.

Best,
Sebastien