You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
{{ message }}
Repository navigation
Open several currently open OME-Zarr images in BDV #108
one LM image, one correlative EM image, and a label mask of the EM image
I think you could just mimic what BigDataViewer is doing at the moment when you say "Open Current Image". It gives you the option to select several of the already currently open images.
Can I just use Plugins › BigDataViewer › Open Current Image to open both of them?
If yes, then maybe we could remove Plugins › OME-Zarr › Open Current OME-Zarr Image in BigDataViewer, because it is redundant, and in fact less powerful because you can only open one image there?!
your intention was correct to question "can do the same". We just checked again and this is actually not the case.
You can in fact use Plugins › BigDataViewer › Open Current Image to open 2 OME-Zarrs from which you have opened two individual zoom levels in Fiji. They will then appear in the same BigDataViewer.
However, when you do so, the images will loose the "awareness" that they are actually part of a multi-resoultion image. The multi-resolution image is aware of these things:
it knows all the resolution levels there are
it also knows about the OMERO metadata (i.e. channel names, contrast limits etc.).
That means that after you have opened an OME-Zarr in BigDataViewer using Plugins › BigDataViewer › Open Current Image, you will not be able from that BigDataViewer window to still use Plugins › OME-Zarr › Open Resolution Level. Also, if you do Plugins › BigDataViewer › Open Current Image, it will never re-use the channel name / contrast limit information of the OME-Zarr.
So:
either Plugins › BigDataViewer › Open Current Image would need to be adapted to keep the awareness of the OME-Zarr multi-resolution and OMERO properties. This would be on the BigDataViewer side of things.
or Plugins › OME-Zarr › Open Current OME-Zarr Image in BigDataViewer needs to be extended to support Images instead of just a single image.
Both options would need to take care of the fact that the BigDataViewer then contains two Multi-Resolution images and we would need to think about what options are provided, if the user wants to do Plugins › OME-Zarr › Open Resolution Level. Then it would need to ask the resolution level of which of the two Multi-resolution images it should open.
You can in fact use Plugins › BigDataViewer › Open Current Image to open 2 OME-Zarrs from which you have opened two individual zoom levels in Fiji. They will then appear in the same BigDataViewer.
However, when you do so, the images will loose the "awareness" that they are actually part of a multi-resoultion image. The multi-resolution image is aware of these things:
just to make sure I understand this: this would be then two SourceAndConverters in BigDataViewer that are multi-resolution, right?
Long term, I think it would be good to get rid of Plugins › OME-Zarr › Open Current OME-Zarr Image in BigDataViewer and just have Plugins › BigDataViewer › Open Current Image
You can in fact use Plugins › BigDataViewer › Open Current Image to open 2 OME-Zarrs from which you have opened two individual zoom levels in Fiji. They will then appear in the same BigDataViewer.
...because the opened OME-Zarrs are all pretending to be also the regular Datasets, so anything that can handle "standard images" will see these images too and can work with them. That's why the Open Current Image works with them, but also treats them like "only the regular datasets" -- that's when Stefan says "However, when you do so, the images will loose the "awareness"...."
just to make sure I understand this: this would be then two SourceAndConverters in BigDataViewer that are multi-resolution, right?
Only the Open Current OME-Zarr Image in BigDataViewer command is ATM aware of the pyramids and opens them as true SACs in BDV, indeed using the multi-resolution.
Long term, I think it would be good to get rid of Plugins › OME-Zarr › Open Current OME-Zarr Image in BigDataViewer and just have Plugins › BigDataViewer › Open Current Image
IMO Agreed! -> Topic for the upcoming hackathon, ping @tpietzsch as we would need changes in the BDV-fiji codebase, I believe.
Only the Open Current OME-Zarr Image in BigDataViewer command is ATM aware of the pyramids and opens them as true SACs in BDV, indeed using the multi-resolution.
I think then a low hanging fruit improvement would be to change this menu entry such that it accepts multiple images as an input (the same way the corresponding BDV menu entry does it).
Cross-reference: #127 asks for the related-but-different variant — adding an OME-Zarr to a BigDataViewer window that is already open (ideally by dragging onto the BDV window), so a second drag & drop does not spawn a second BDV.
This issue is the batch at open time case: several already-open OME-Zarr images → one new BDV, pyramid- and OMERO-aware.
Overlap: both end with more than one source in one BDV, and both need the same answer to "which multi-resolution image does Plugins › OME-Zarr › Open Resolution Level act on?".
The low-hanging fruit is in #150: with several OME-Zarrs open, Plugins › OME-Zarr › Open Current OME-Zarr Image in BigDataViewer now asks which of them to show, like BDV's "Open Current Image", and shows them multi-resolution and with their OMERO settings in one BDV window. Making BDV's own command pyramid-aware still needs changes on the BigDataViewer side.
Closing, since #150 delivered the "low-hanging fruit": several open OME-Zarrs go into one BDV, multi-resolution and with OMERO settings (see above). Replacing our Plugins › OME-Zarr › Open Current OME-Zarr Image in BigDataViewer with BDV's own Plugins › BigDataViewer › Open Current Image needs a change on the BigDataViewer side and continues in #161.
Activity
stefanhahmann commentedon Sep 1, 2026
At the moment not. Can you specify a bit more what you mean by "together"?
Are these several images:
of the "same" image
or are these multiple images tiles of an even bigger image?
tischi commentedon Sep 2, 2026
Those are totally separate OME-Zarr.
Use-cases:
I think you could just mimic what BigDataViewer is doing at the moment when you say "Open Current Image". It gives you the option to select several of the already currently open images.
Plugins › BigDataViewer › Open Current Imagestefanhahmann commentedon Sep 2, 2026
Ah, I see. Now I understand.
This is actually possible already.
You can open e.g. https://livingobjects.ebi.ac.uk/idr/zarr/v0.5/idr0033A/BR00109990_C2.zarr/0 as an image in Fiji and e.g. https://livingobjects.ebi.ac.uk/idr/zarr/v0.5/idr0033A/BR00109990_C2.zarr/1 (This is not really a good example, since these examples were orignally not overlaying each other, but for technial demonstration, it is sufficient).
Then you have both images opened in Fiji just like in your example and then you can do the same. So, it should work also with OME-Zarrs that way.
Can you confirm that this is sufficient for your use case? Sorry for the initial misunderstanding.
tischi commentedon Sep 2, 2026
Hi, what do you mean I "can do the same"?
Can I just use
Plugins › BigDataViewer › Open Current Imageto open both of them?If yes, then maybe we could remove
Plugins › OME-Zarr › Open Current OME-Zarr Image in BigDataViewer, because it is redundant, and in fact less powerful because you can only open one image there?!stefanhahmann commentedon Sep 2, 2026
Hi @tischi
your intention was correct to question "can do the same". We just checked again and this is actually not the case.
You can in fact use
Plugins › BigDataViewer › Open Current Imageto open 2 OME-Zarrs from which you have opened two individual zoom levels in Fiji. They will then appear in the same BigDataViewer.However, when you do so, the images will loose the "awareness" that they are actually part of a multi-resoultion image. The multi-resolution image is aware of these things:
That means that after you have opened an OME-Zarr in BigDataViewer using
Plugins › BigDataViewer › Open Current Image, you will not be able from that BigDataViewer window to still usePlugins › OME-Zarr › Open Resolution Level. Also, if you doPlugins › BigDataViewer › Open Current Image, it will never re-use the channel name / contrast limit information of the OME-Zarr.So:
Plugins › BigDataViewer › Open Current Imagewould need to be adapted to keep the awareness of the OME-Zarr multi-resolution and OMERO properties. This would be on the BigDataViewer side of things.Plugins › OME-Zarr › Open Current OME-Zarr Image in BigDataViewerneeds to be extended to support Images instead of just a single image.Both options would need to take care of the fact that the BigDataViewer then contains two Multi-Resolution images and we would need to think about what options are provided, if the user wants to do
Plugins › OME-Zarr › Open Resolution Level. Then it would need to ask the resolution level of which of the two Multi-resolution images it should open.tischi commentedon Sep 2, 2026
just to make sure I understand this: this would be then two SourceAndConverters in BigDataViewer that are multi-resolution, right?
Long term, I think it would be good to get rid of
Plugins › OME-Zarr › Open Current OME-Zarr Image in BigDataViewerand just havePlugins › BigDataViewer › Open Current Imagexulman commentedon Sep 2, 2026
...because the opened OME-Zarrs are all pretending to be also the regular
Datasets, so anything that can handle "standard images" will see these images too and can work with them. That's why theOpen Current Imageworks with them, but also treats them like "only the regular datasets" -- that's when Stefan says "However, when you do so, the images will loose the "awareness"...."xulman commentedon Sep 2, 2026
Only the
Open Current OME-Zarr Image in BigDataViewercommand is ATM aware of the pyramids and opens them as trueSACs in BDV, indeed using the multi-resolution.xulman commentedon Sep 2, 2026
IMO Agreed! -> Topic for the upcoming hackathon, ping @tpietzsch as we would need changes in the BDV-fiji codebase, I believe.
tischi commentedon Sep 2, 2026
I think then a low hanging fruit improvement would be to change this menu entry such that it accepts multiple images as an input (the same way the corresponding BDV menu entry does it).
stefanhahmann commentedon Sep 22, 2026
Cross-reference: #127 asks for the related-but-different variant — adding an OME-Zarr to a BigDataViewer window that is already open (ideally by dragging onto the BDV window), so a second drag & drop does not spawn a second BDV.
This issue is the batch at open time case: several already-open OME-Zarr images → one new BDV, pyramid- and OMERO-aware.
Overlap: both end with more than one source in one BDV, and both need the same answer to "which multi-resolution image does
Plugins › OME-Zarr › Open Resolution Levelact on?".stefanhahmann commentedon Oct 12, 2026
The low-hanging fruit is in #150: with several OME-Zarrs open,
Plugins › OME-Zarr › Open Current OME-Zarr Image in BigDataViewernow asks which of them to show, like BDV's "Open Current Image", and shows them multi-resolution and with their OMERO settings in one BDV window. Making BDV's own command pyramid-aware still needs changes on the BigDataViewer side.stefanhahmann commentedon Oct 27, 2026
Closing, since #150 delivered the "low-hanging fruit": several open OME-Zarrs go into one BDV, multi-resolution and with OMERO settings (see above). Replacing our
Plugins › OME-Zarr › Open Current OME-Zarr Image in BigDataViewerwith BDV's ownPlugins › BigDataViewer › Open Current Imageneeds a change on the BigDataViewer side and continues in #161.