I am labelling some nuclei manually using labkit to eventually use as training data for stardist. When testing my data (stardist/examples/3D at master · stardist/stardist · GitHub) with the example it showed the X-Z slices looked distorted, like they lost their original properties.
I am trying to solve this issue and started to have a look in labkit itself
When trying to look at the XZ axis labelling in labkit I ran into some problems:
-Is it possible to switch to a XZ-axis view inside labkit ánd go through the slices easily, while XZ properties are maintained?
On the stardist website it was recommended to switch z and t (via reorder hyperstacks) before going into labkit to go easily thorugh the z-slices (using [ and ]). With these settings it is not possible to rotate the image inside labkit anlymore to have a look at the XZ-axis.
If I do not apply these settings (switching z and t), it is possible. Nevertheless, the Z-slices look distorted inside labkit as well (like they have lost their properties also). Also, it is not possible to navigate easily through the Z-slices anymore, showing slice numbers like 6.4 and 6.7, like there are slices inbetween my actual slices.
An example of my view of the XZ axis inside labkit:
-Does anyone know how to explain why the slice coordinates have comma numbers? (also in the normal XY view this is the case, when not reordering hyperstacks and switching z and t)
-Does anyone know why my XZ properties are not maintained?