Can not saving 3D tiff format for layer

[jinxsfe]

🐛 Bug Report

I try to create the label point and make annotation and process images, but when I do several of step,and I click save all layer or save select layer

File ~/miniconda3/envs/napari-env/lib/python3.10/site-packages/napari_svg/layer_to_xml.py:104, in image_to_xml(data=<class 'numpy.ndarray'> (140, 464, 464) float32, meta={'affine': <class 'numpy.ndarray'> (4, 4) float64, 'attenuation': 0.05, 'blending': 'translucent_no_depth', 'colormap': 'gray', 'contrast_limits': [-0.5080329775810242, 0.6496055126190186], 'custom_interpolation_kernel_2d': <class 'numpy.ndarray'> (1, 1) float32, 'depiction': 'volume', 'experimental_clipping_planes': [], 'gamma': 1, 'interpolation2d': 'nearest', ...})
102 # Check if more than 2 dimensional and if so error.
103 if data.ndim - int(rgb) > 2:
--> 104 raise ValueError(f'Image must be 2 dimensional, not {data.ndim - int(rgb)} to save as svg')
data = <class 'numpy.ndarray'> (140, 464, 464) float32
rgb = False
int(rgb) = 0
105 else:
106 image = data

ValueError: Image must be 2 dimensional, not 3 to save as svg

Does anyone know how to save 3D stack into tiff format?

best

💡 Steps to Reproduce

go to file
click save select layer or select all layer

Does anyone know how to save 3D stack into tiff format?

best

💡 Expected Behavior

give me some guidence

🌎 Environment

linux ubuntu

💡 Additional Context

s

[jinxsfe]

@stefanv @zeroth @joshmoore @hmaarrfk

[jinxsfe]

also I tried another way to export file, but also not working

[jinxsfe]

data is 440440140, can not generate 3D image but csv file

[psobolewskiPhD]

I'm not sure why the default is the svg writer (cc: @DragaDoncila ), but in the Save Selected or Save All dialog (File menu) you should be able to select Save to folder. Here's what it looks like on macOS:

You can give a name and napari will create a folder with that name and put your layers inside, e.g.:

Hope that helps!

[jinxsfe]

Hi: appreciate for your help:
my machine is ubuntu, instead of mac OS.
and I try to save those file in my machine



it seems ok for now, but my confusion is that why I can not save points layer as tiff files? actually I want to annotate the data via point but seems only generate CSV files instaead of tiff format.

[jinxsfe]

also my directory can save builtin save format

[Czaki]

Tiff is a format for storing n-dimensional arrays, not a list of points.
We currently support saving points to csv.

I do not even have idea how we could store points in tiff file.

[psobolewskiPhD]

@jinxsfe
I've opened an issue regarding the svg writer:
#6846

Regarding the csv, they container the coordinates of the points--the points data.
(You can do viewer.layers['Points'].data to see it -- where Points is the name of the points layer.)
If you drag and drop the tiff of your image and the Points csv file on napari, you will get the points back.
The actual Points markers (the disc or diamond or whatever) only exists on the GPU. If you want to save that representation you need to use the napari screenshot options (File menu).