Open Microscopy Environment

Hey,

I am currently using Bio-Formats with ImageJ (Fiji installation to be exact) to analyze a test scan, saved in .vsi file. I can easily open the .vsi file using Bio-Formats Importer and see all the series inside. However I am unable to import the ROI data saved within the file (that I know exists in there on a separate layer, as can be seen in OlyVIA). Even if I enable the display_roi and rois_import=[ROI manager] options, nothing is imported into ROI Manager no matter which series I try.

When I import the series, for example the largest 40x scans, I can see in Metadata that there are 3 layers: "40x", "40x FocusMap", and "Measurement and ROI". The third layer has the same name as the metrics layer in OlyVIA, though I could not find anything on layer handling.

Am I missing something here? How to import ROIs saved in CellSens .vsi files?

Thanks

I'm afraid that the existing CellSensReader does not have complete support for ROIs. The ticket for this missing functionality is #5396.

If you would like to upload an example with ROIs using our upload page we can certainly add this to the existing set of files with ROIs (I think we only have one contrived example in the above ticket, so more realistic examples would certainly be appreciated).

Unfortunately, supporting complex proprietary file formats is very time-consuming and difficult, and I would suggest reading our format support blog post detailing our current policy for supporting proprietary formats such as CellSens. You might also find these of related interest: open collaborations and Bio-Formats development status. The summary of the above would be that we lack the resources to support every feature of closed, proprietary file formats, and it's unlikely that we would commit to implementing the feature ourselves. However, we would be able to review, test and integrate the feature if implemented and submitted by a third party, as has been done for several other file formats. This could be paid for through a company like Glencoe Software, developed by an end user or even be done by Olympus should they wish to improve the wider support for their own file format.

Kind regards,
Roger