Tiled .LIF file problems

[Oli]

Dear Melissa et al.

For a while now we've been plagued with a modification to the .lif format which is as follows

For tiled images, the .lif file used to contain N series of images, corresponding to each XYCZT stack position that was tiled, which was great.

Now Leica have added a "Planes" dimension to their series, meaning that a single series now contains XYZCTP information, which BioFormats mistakenly considers to be 'Time' instead of a 'Plane'.

In itself that isn't a problem, however we are incapable of reading the coordinates of the plane positions, because they are all identical, which makes stitching much more difficult.
Looking at the original metadata, we see that the XYZ coordinates are there, albeit probably not in the format that LOCI was expecting.

If you think you could work on this problem, please let me know. I can also get you in touch with a Leica representative who said there should be no problem in providing you with the description of the .lif format. I can also provide a dataset (19Gb though...)

Thank you again for your time and if you could let me know as soon as possible that would be extremely helpful.

All the best

Oli

[mlinkert]

Hi Oli,

Thanks for reporting this. As usual, the best thing to do is to send the file - to my knowledge, we don't have any .lif files with multiple "Planes". I think I have sent you FTP server information in the recent past, but if not please let me know and I will send it in a private message.

-Melissa

[Oli]

My bad, in their slang it's "series".

But unlike the previous LIF files, the one I'm uploading now opens properly in the LAS AF lite

but instead of hainv several independent "series" files (each corresponding to a position in xyczt)
it contains a single 'series' (as per the usual definition), defined by xyczts, 's' being the culprit here.

Hopefully the file will be uploaded by this afternoon. (bob.lif)

As usual thanks again!

Oli

[mlinkert]

Hi Oli,

Thank you for uploading a file.

There is now a ticket on our issue tracking system:

http://trac.openmicroscopy.org.uk/ome/ticket/10634

I expect that we will have this fixed in the next version of Bio-Formats.

-Melissa

[Oli]

Dear Melissa,

Thank you for the feedback. I have provided a smaller image type for tests if needed (Mike).

I also downloaded the daily build. It detects the series properly but (for now at least), they all have exactly the same XY coordinates.

All the best!

Oli

[mlinkert]

Hi Oli,

Thank you for uploading an additional (and much more manageable!) file.

A fix for the tile position problem is under review here:

https://github.com/openmicroscopy/bioformats/pull/521

I'd expect that to be resolved soon and included in the next release.

-Melissa

[Oli]

Dear Melissa,

It seems that we have an interesting problem again with a very large dataset.
It is a set containing >700 series of 3D stacks.

In the .lif there is only 1 series with xyzs = 1024, 1024, 48, 784

The number gets detected properly by LOCI and then prompts to open the series by entering a list of numbers.
No matter what number I put in, it always imports the first z stack and when I select a range, some of the opened series are duplicated, and others are OK.

When opening the .lif file using LAS AF, everything works fine...

[mlinkert]

Hi Oli,

Does the same problem occur if you use the builds from http://hudson.openmicroscopy.org.uk/vie ... artifacts/?

If not, would you be willing to upload the file (or a smaller file that demonstrates the same issue)?

Regards,
-Melissa

[Oli]

Hi all,

Sorry for reviving this old thread. The old issues seem to have been fixed a while back. However today we have a new problem with tiled LIF files

When opening a multiposition LIF file in Bioformats, there seems to be a corruption on the file indexes.

When I open this 4x8 tile in LAS-AF Lite, I can see each z stack tile no problem. However, importing it in Fiji with Bioformats seems to cause an offset problem, after the 7th series, it loops back to the first image and every next image is strangely offset (The image ends midway and the next image starts).

I would like to provide a sample dataset but it is ~10GB, so unless you can provide me with a link where I can drop it off, I am a bit stuck at the moment.

All the best

Oli

[mlinkert]

Hi Oli,

I will send alternate upload instructions in a private message.

-Melissa