Comments (2)
Thanks for reporting, I'll address this. Longer term, I'd like to give users control about axis/dimension order. (see issue #45).
For the time being, you can work around it with a macro:
run("Properties...", "channels=1 slices=30 frames=5 pixel_width=1.0000 pixel_height=1.0000 voxel_depth=1.0000");
run("Re-order Hyperstack ...", "channels=[Frames (t)] slices=[Slices (z)] frames=[Channels (c)]");
Short explanation + caveat:
Since imageJ's dimensions have meaning (XYCZT) and zarr's don't, the current plugin doesn't promise the dimensions will be ordered "correctly" in imageJ unless using a supported metadata format (and there are not many of them); otherwise it makes a guess. In your case, it actually guessed correctly, but in the process messed up the interleaving of slices - causing the problem you observed. and that is a bug. I.e. correct behavior using this version would be for your image to open with 30 channels and 5 slices, but without the interleaving problem.
Note to self: look here.
from n5-ij.
I believe this is what I'm experiencing with my 4D dataset too. Moving either the c and z sliders change both the c and z values.
from n5-ij.
Related Issues (20)
- Fiji warning when pulling data from S3
- strange behavior using jq translation with hdf5 backends
- Add panel for inverse translation
- Exeception when saving as .zarr HOT 4
- Progress bar while file saving HOT 2
- Feature request: option to generate multichannel/multiscale during export HOT 1
- ImagePlus getOriginalFileInfo should be useful
- Issue trying to open hdf5 images exported by BigStitcher HOT 1
- Opening N5 is slow
- Support OME-NGFF metadata and group structure HOT 2
- Paintera label-multiset datasets cannot be opened HOT 1
- Threadpool not being "joined" in n5 save()? HOT 6
- Consistency between FIJI GUI and N5IJUtils.load()
- Warn users if an array exists, allow overwriting HOT 1
- OME-Zarr containers do not parse when nested inside other paths HOT 4
- Unit should be "micrometer" for compatbility with OME-NGFF HOT 1
- Intermittent test failure HOT 1
- Invalid path in Import > HDF5/N5/Zarr/OME-NGFF ... crop dialog HOT 2
- Issue opining up h5 file using N5 plugin - images are blank HOT 3
- Support for non-standard port numbers
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from n5-ij.