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InCarta File format for Mobie-Viewer ? #1137

Closed ThomasMicroscopy closed 2 weeks ago

ThomasMicroscopy commented 1 month ago

Is it possible to open IN Carta files (.xdce Metafile) with Mobie-Viewer? I gave it a try in Fiji with Mobie, but didn't seem to work.

Molecular Devices is now favouring their IN Carta software with AI, which has a slightly different file format than their MetaXpress file format (.htd). We would be quite interested in using a Plate Viewer for IN Carta files, as IN Carta does not use a SQL database anymore (in contrast to MetaXpress), which makes storing and archiving easier for us.

tischi commented 1 month ago

Hi Thomas,

I unfortunately don't have the time (nor personell) to add support for new file formats.

I think the only sustainable way forward here would be see whether Bio-Formats can convert the file-format to the OME-Zarr HCS specification, which is supported by MoBIE.

@bugraoezdemir @joshmoore do you know about "IN Carta files (.xdce Metafile)" file format support in Bio-Formats?

If this is not supported by Bio-Formats then one should tell the company to make that happen!

ThomasMicroscopy commented 2 weeks ago

Actually, given that the .htd format gave such troubles so that you bypassed the Bio-Formats importer, if I understood you correctly, maybe it would work with the In Carta files as well, just parsing the tif files?

Screenshot 2024-06-17 at 13 21 23
tischi commented 2 weeks ago

Yes, that should work as well; could you share a minimal test data set with me?

ThomasMicroscopy commented 2 weeks ago

Ok, I prepare a small set. If it works just on the TIFs, that would also solve the issue that IN Carta itself converts vom .xdce to jdce, but without touching the TIFs.

ThomasMicroscopy commented 2 weeks ago

The dataset I just sent includes also some z-planes. Can MoBIE deal with z-planes, I forgot. I guess it's enough to just select one z-plane and display that. The images in the set I sent are very boring, and empty plate, just dirt and dust....

joshmoore commented 2 weeks ago

From the information on https://forum.image.sc/t/support-for-in-carta-hcs-files/97144/2 I'd say what's happened is that a new variant/format has now been created on top of .xdce. 😞

ThomasMicroscopy commented 2 weeks ago

Yes, indeed. I had only recently noticed that the xdce disappears after In Carta opens it. But if the tif files can be read in plate format by MoBIE just based parsing the file names, without either xdce, or jdce, then it would not matter.

tischi commented 2 weeks ago

Does that look good? One can even go through the different z-planes (using the mouse wheel).

image
ThomasMicroscopy commented 2 weeks ago

Yes, looks right (don't remember if e04 is so dark), it's just an empty plate, so you see dirt, and out of focus dirt.

tischi commented 2 weeks ago

OK, I uploaded the changes; if you update Fiji you could try yourself.

ThomasMicroscopy commented 2 weeks ago

Hmm, it updated MoBIE, but it generates an error, with basically the same dataset. smallIMG_2056

ThomasMicroscopy commented 2 weeks ago

Does the problem have anything to do that the button to open the file search dialog is missing?

tischi commented 2 weeks ago

Does the problem have anything to do that the button to open the file search dialog is missing?

Nope, I will make that button reappear.

but it generates an error, with basically the same dataset.

Strange, let me check....

tischi commented 2 weeks ago

I uploaded a new version that will output a more informative error message.

Could you please run it again and post the new error message here?

The best would be if you copy and paste the actual text rather than posting a screenshot.

ThomasMicroscopy commented 2 weeks ago

No need for error message ;-) It works with MetaXpress .TIF files, and with IN Carta .TIF files (both the .xdce, and the jdce). The dialog box is back too. Great! Thank you very much!

A question regarding the zoom function. On the PC I was using it, when using the scroll wheel, with a 2D dataset, the scroll wheel would zoom in and out. According to the help instruction, zoom should work with ctrl-shift scroll wheel, it does. When I was loading now a 3D dataset, with z-stack, the using the scroll wheel, it turned black when clicking one position off. Turning it one click back, returned the 2D layout of the plate. (when scrolling more, it stayed black, presumably because I couldn't find the right layer anymore.) Is that a problem with using the scroll wheel, or is it an issue that the z-stack is not displayed properly?

Also, how to deal with memory issues. A plate dataset can be quite large, more than RAM. For example, a 384 well plate, with 3x3 sites, and 3 wavelengths, is already >10'000 pictures. Not sure which dataset it was, but when I was moving around, zooming in and out on wells, eventually I got numerous "Exception in thread "Fetcher - X" [X a number] java.lang.OurOfMemoryError: Java heap space. It slowed down a lot, but I was still able to quit the program regularly. Any tips how to deal with this?

Thanks again for making this work.

tischi commented 2 weeks ago

I will close this issue then and make new ones.