Open Microscopy Environment

Dear OME Team,
I found two problems with reading metadata in tiff files generated from Andor's IQ3 software.
1. Acquisition date gets wrong in OME.xml block; months and days are swapped. And if the day is higher than 12th, there is no acquisition date given. I will upload two files created on different occasions to demonstrate this.
2. User's comments are written to the Andor's metadata block between [Comments] and [Comments End] inside the ImageDescription Tag #270, together with other metadata (exemplary user's comments are included in uploaded files). However, this information is lost after import with Bioformats; <Description> element under <Image> element is empty. Any chance to place user's comments there? If I had to do it myself, which tools would be most appropriate in this case to customize parsing (I have very basic programming skills, but I am eager to improve them ?
Thanks!
Tomasz

Hi Thomasz,

thanks for reaching us and uploading some sample files.

1. Acquisition date gets wrong in OME.xml block; months and days are swapped. And if the day is higher than 12th, there is no acquisition date given. I will upload two files created on different occasions to demonstrate this.

This completely makes sense given the samples you uploaded. The original feature for reading acquisition date and the date pattern was introduced in this commit. Unfortunately, the original specification which we used contains the following:

Date=03-17-2001 Time and date file was saved

So it seems we have date patterns with different positions of the day and month. There might be two causes: either the format specification went through a breaking format change or the format of the date could be system-specific. Do you happen to know if it is possible to change the formats of the latter?

2. User's comments are written to the Andor's metadata block between [Comments] and [Comments End]

The logic in the reader which fills the Image Description is here. Currently we are filling it with the content of the [Version Info] block. We could look into using handling the Comments block (unless you are interested in giving a try).

Best regards,
Sebastien

So it seems we have date patterns with different positions of the day and month. There might be two causes: either the format specification went through a breaking format change or the format of the date could be system-specific. Do you happen to know if it is possible to change the formats of the latter?

Dear Sebastien,
The tiff images are exports from Andor's IQ3 software and Andor obviously sticks to the European date format, e.g.:

Code: Select all

[Created]
Date=26/09/2014
Time=12:07:26
[Created End]

I cannot speak in their name but I do not think they would be willing to change that.
Best,
Tomasz

Hi Tomasz,

thanks very much for the precisions. Note that a complication arises from the fact that the same file reader is used for two separate but extremely similar formats: Andor ABD TIFF and Olympus FluoView TIFF.

We are in contact with people from Andor to confirm the format expectations from their side. We will be updating the status of this issue using the following Trello card.

Best,
Sebastien

Dear Sebastien,
I understand that from your side correcting the date formatting may be more problematic because the updated reader should be fully compatible with both file formats. In my situation, it is not a problem, we need FluoviewReader only for Andor files. So, I corrected the date formatting in the source java file and replaced [Version Info] with [Comments], compiled, updated the jar file, and it seems to work fine now, at least in Fiji on my PC. But if this works here, it should also work on omero. I guess, I should update both copies of formats-gpl.jar files, in the client and server folders, right?
I also realized the xml elements are single line (and the reader trims everything past the first line), so I will have to tell users not to press ENTER while writing comments in IQ3 (the comments can be multiline in IQ3).
Anyway, thanks a lot for your help, I think it should work now, if not I will come back here with more questions.
best,
Tomasz

Hi Thomasz

I understand that from your side correcting the date formatting may be more problematic because the updated reader should be fully compatible with both file formats. In my situation, it is not a problem, we need FluoviewReader only for Andor files.

Absolutely. From our side, once we have checked the proposed changes are harmless, we'll be looking into integrating the date formatting fix minimally into a patch release of Bio-Formats 5.4.x. Please let us know if are interested into contributing directly via a Pull Request or at sharing your patch so that we can commit it on your behalf.

So, I corrected the date formatting in the source java file and replaced [Version Info] with [Comments], compiled, updated the jar file, and it seems to work fine now, at least in Fiji on my PC.

Excellent.

But if this works here, it should also work on omero. I guess, I should update both copies of formats-gpl.jar files, in the client and server folders, right?

Yes, replacing the formats-gpl jars under the various `lib/` folders of an existing server should work as expected in your case. Alternatively, you can rebuild the whole server using your local version of Bio-Formats (see the developer documentation for more instructions).

I also realized the xml elements are single line (and the reader trims everything past the first line), so I will have to tell users not to press ENTER while writing comments in IQ3 (the comments can be multiline in IQ3).

Agreed. This is potentially another limitation that we can review and address in the future.

Anyway, thanks a lot for your help, I think it should work now, if not I will come back here with more questions.

Thanks for your feedback and engagement.

Best,
Sebastien

Quick update on this thread. The acquisition date should now be correctly parsed for Andor's IQ3 TIFF files with the release of Bio-Formats 5.5.0.