Points are not showing on the viewer

I tried to use the napari viewer and display points but points are not showing.
I see the points on the thumbnails but not on the viewer.

I ran the script described in
Point selection with shapes layer + Shapely to test the visualization of point but they don’t appear

I used Anaconda 2020.02 (come with python 3.7) 64bits last installer on windows, which comes with QT library 5.9.6

Hi @bpavie, sorry that you’re running into this problem. I was just able to run the script that you linked and was able to see the points and verify that the shapely selection functionality worked as expected, see the screenshot below after drawing a polygon and pressing f to highlight:

When you first run the script do you just see a black screen (i.e. no white points)? It looks like in your example you’ve already drawn a triangle in the shapes layer, I’m just curious if you ever saw anything before drawing - in case something weird is happening with the zoom and if you zoomed out / panned you would see the points.

If that doesn’t seem to be it, maybe you can try running our examples/add_points.py to verify you see points there. Maybe also you can paste the exact code you ran into this issue in case there was a copy paste error for the link you provided. We should be able to get this working.


Hi @sofroniewn, thanks for your answer.
Running your example script doesn’t display the points as well on the viewer (I just can see that a points layer have been created) I think the points are here but somehow not visible…


Could you copy-paste the information found in the top panel of Help menu > napari info?

Hi @jni, here they are:

napari: 0.2.12
Platform: Windows-10-10.0.17763-SP0
Python: 3.7.6 (default, Jan 8 2020, 20:23:39) [MSC v.1916 64 bit (AMD64)]
Qt: 5.9.6
PyQt5: 5.9.2
VisPy: 0.6.4
NumPy: 1.18.1
SciPy: 1.4.1
scikit-image: 0.16.2
Dask: 2.11.0

GL version: 4.0.0 - Build

Hmm - I don’t think we’ve seen this before. I wonder if it is your GL version - mine is GL version: 2.1 INTEL-14.4.23. We use vispy under the hood for our rendering and it might not work with 4.0.0.

I’m curious if the examples/add_shapes.py works (you should see some shapes). I’m also curious if you change the symbol in the points layer are there any that work or do they all fail?

I might try and give you a minimal vispy example using their Markers visual (which we use for our Points layer) to see if the problem is there or within napari. If the problem ends up inside vispy we can raise a dedicated issue there, otherwise we can work on it within napari

Thanks @sofroniewn

I tested the examples/add_shapes.py and it works, I only have issue with the points.

Here is my opengl version:

from OpenGL.GL import GL_VERSION
from OpenGL.raw.GL.VERSION.GL_1_1 import glGetString

b'4.0.0 - Build'

Hmm ok, I think the next step is to try and put together a minimal vispy only demo using their Markers visual to see if you can visualize that. It looks like Mesh and Image are working fine for you. Let me know if you put this together, otherwise I will make one and post it here for you when I can.