Napari stops working after importing umap data

[saugatkandel]

I am following the tutorial steps, and have napari-tomotwin installed using the following command:
mamba env create -n napari-tomotwin -f https://raw.githubusercontent.com/MPI-Dortmund/napari-tomotwin/main/conda_env.yml

I can load the UMAP data into napari. At this point, my napari window looks like:

Now, when I click on the tomogram, I immediately get the error message:

------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
File /hpc/projects/group.czii/saugat.kandel/miniforge3/envs/napari-tomotwin/lib/python3.10/site-packages/vispy/app/backends/_qt.py:496, in QtBaseCanvasBackend.mousePressEvent(self=<vispy.app.backends._qt.CanvasBackendDesktop object>, ev=<PyQt5.QtGui.QMouseEvent object>)
    494 if self._vispy_canvas is None:
    495     return
--> 496 self._vispy_mouse_press(
        self = <vispy.app.backends._qt.CanvasBackendDesktop object at 0x7f0c800ae290>
        ev = <PyQt5.QtGui.QMouseEvent object at 0x7f0c2a556d40>
        BUTTONMAP = {0: 0, 1: 1, 2: 2, 4: 3, 8: 4, 16: 5}
    497     native=ev,
    498     pos=_get_event_xy(ev),
    499     button=BUTTONMAP.get(ev.button(), 0),
    500     modifiers=self._modifiers(ev),
    501 )

File /hpc/projects/group.czii/saugat.kandel/miniforge3/envs/napari-tomotwin/lib/python3.10/site-packages/vispy/app/base.py:184, in BaseCanvasBackend._vispy_mouse_press(self=<vispy.app.backends._qt.CanvasBackendDesktop object>, **kwargs={'button': 1, 'buttons': [], 'last_event': <MouseEvent blocked=False button=None buttons=[]...urces=[] time=1716403732.2130306 type=mouse_move>, 'last_mouse_press': None, 'modifiers': (), 'native': <PyQt5.QtGui.QMouseEvent object>, 'pos': (692, 600), 'press_event': None})
    181 def _vispy_mouse_press(self, **kwargs):
    182     # default method for delivering mouse press events to the canvas
    183     kwargs.update(self._vispy_mouse_data)
--> 184     ev = self._vispy_canvas.events.mouse_press(**kwargs)
        self._vispy_canvas.events.mouse_press = <vispy.util.event.EventEmitter object at 0x7f0c800bc1f0>
        kwargs = {'native': <PyQt5.QtGui.QMouseEvent object at 0x7f0c2a556d40>, 'pos': (692, 600), 'button': 1, 'modifiers': (), 'buttons': [], 'press_event': None, 'last_event': <MouseEvent blocked=False button=None buttons=[] delta=[0. 0.] handled=False is_dragging=False last_event=None modifiers=() native=<PyQt5.QtGui.QMouseEvent object at 0x7f0c2a556d40> pos=[692 600] press_event=None source=None sources=[] time=1716403732.2130306 type=mouse_move>, 'last_mouse_press': None}
        self = <vispy.app.backends._qt.CanvasBackendDesktop object at 0x7f0c800ae290>
        self._vispy_canvas.events = <vispy.util.event.EmitterGroup object at 0x7f0c800bc1c0>
        self._vispy_canvas = <VispyCanvas (PyQt5) at 0x7f0c800ab850>
    185     if self._vispy_mouse_data['press_event'] is None:
    186         self._vispy_mouse_data['press_event'] = ev

File /hpc/projects/group.czii/saugat.kandel/miniforge3/envs/napari-tomotwin/lib/python3.10/site-packages/vispy/util/event.py:453, in EventEmitter.__call__(self=<vispy.util.event.EventEmitter object>, *args=(), **kwargs={'button': 1, 'buttons': [], 'last_event': <MouseEvent blocked=False button=None buttons=[]...urces=[] time=1716403732.2130306 type=mouse_move>, 'last_mouse_press': None, 'modifiers': (), 'native': <PyQt5.QtGui.QMouseEvent object>, 'pos': (692, 600), 'press_event': None})
    450 if self._emitting > 1:
    451     raise RuntimeError('EventEmitter loop detected!')
--> 453 self._invoke_callback(cb, event)
        event = <MouseEvent blocked=False button=1 buttons=[1] delta=[0. 0.] handled=False is_dragging=False last_event=MouseEvent modifiers=() native=<PyQt5.QtGui.QMouseEvent object at 0x7f0c2a556d40> pos=[692 600] press_event=None source=None sources=[] time=1716403732.224965 type=mouse_press>
        self = <vispy.util.event.EventEmitter object at 0x7f0c800bc1f0>
        cb = <bound method QtViewer.on_mouse_press of <napari._qt.qt_viewer.QtViewer object at 0x7f0c800a2b90>>
    454 if event.blocked:
    455     break

File /hpc/projects/group.czii/saugat.kandel/miniforge3/envs/napari-tomotwin/lib/python3.10/site-packages/vispy/util/event.py:471, in EventEmitter._invoke_callback(self=<vispy.util.event.EventEmitter object>, cb=<bound method QtViewer.on_mouse_press of <napari._qt.qt_viewer.QtViewer object>>, event=<MouseEvent blocked=False button=1 buttons=[1] d...urces=[] time=1716403732.224965 type=mouse_press>)
    469     cb(event)
    470 except Exception:
--> 471     _handle_exception(self.ignore_callback_errors,
        self = <vispy.util.event.EventEmitter object at 0x7f0c800bc1f0>
        cb = <bound method QtViewer.on_mouse_press of <napari._qt.qt_viewer.QtViewer object at 0x7f0c800a2b90>>
        event = <MouseEvent blocked=False button=1 buttons=[1] delta=[0. 0.] handled=False is_dragging=False last_event=MouseEvent modifiers=() native=<PyQt5.QtGui.QMouseEvent object at 0x7f0c2a556d40> pos=[692 600] press_event=None source=None sources=[] time=1716403732.224965 type=mouse_press>
        (cb, event) = (<bound method QtViewer.on_mouse_press of <napari._qt.qt_viewer.QtViewer object at 0x7f0c800a2b90>>, <MouseEvent blocked=False button=1 buttons=[1] delta=[0. 0.] handled=False is_dragging=False last_event=MouseEvent modifiers=() native=<PyQt5.QtGui.QMouseEvent object at 0x7f0c2a556d40> pos=[692 600] press_event=None source=None sources=[] time=1716403732.224965 type=mouse_press>)
    472                       self.print_callback_errors,
    473                       self, cb_event=(cb, event))

File /hpc/projects/group.czii/saugat.kandel/miniforge3/envs/napari-tomotwin/lib/python3.10/site-packages/vispy/util/event.py:469, in EventEmitter._invoke_callback(self=<vispy.util.event.EventEmitter object>, cb=<bound method QtViewer.on_mouse_press of <napari._qt.qt_viewer.QtViewer object>>, event=<MouseEvent blocked=False button=1 buttons=[1] d...urces=[] time=1716403732.224965 type=mouse_press>)
    467 def _invoke_callback(self, cb, event):
    468     try:
--> 469         cb(event)
        cb = <bound method QtViewer.on_mouse_press of <napari._qt.qt_viewer.QtViewer object at 0x7f0c800a2b90>>
        event = <MouseEvent blocked=False button=1 buttons=[1] delta=[0. 0.] handled=False is_dragging=False last_event=MouseEvent modifiers=() native=<PyQt5.QtGui.QMouseEvent object at 0x7f0c2a556d40> pos=[692 600] press_event=None source=None sources=[] time=1716403732.224965 type=mouse_press>
    470     except Exception:
    471         _handle_exception(self.ignore_callback_errors,
    472                           self.print_callback_errors,
    473                           self, cb_event=(cb, event))

File /hpc/projects/group.czii/saugat.kandel/miniforge3/envs/napari-tomotwin/lib/python3.10/site-packages/napari/_qt/qt_viewer.py:1201, in QtViewer.on_mouse_press(self=<napari._qt.qt_viewer.QtViewer object>, event=<MouseEvent blocked=False button=1 buttons=[1] d...urces=[] time=1716403732.224965 type=mouse_press>)
   1193 def on_mouse_press(self, event):
   1194     """Called whenever mouse pressed in canvas.
   1195 
   1196     Parameters
   (...)
   1199         The vispy event that triggered this method.
   1200     """
-> 1201     self._process_mouse_event(mouse_press_callbacks, event)
        event = <MouseEvent blocked=False button=1 buttons=[1] delta=[0. 0.] handled=False is_dragging=False last_event=MouseEvent modifiers=() native=<PyQt5.QtGui.QMouseEvent object at 0x7f0c2a556d40> pos=[692 600] press_event=None source=None sources=[] time=1716403732.224965 type=mouse_press>
        self = <napari._qt.qt_viewer.QtViewer object at 0x7f0c800a2b90>

File /hpc/projects/group.czii/saugat.kandel/miniforge3/envs/napari-tomotwin/lib/python3.10/site-packages/napari/_qt/qt_viewer.py:1156, in QtViewer._process_mouse_event(self=<napari._qt.qt_viewer.QtViewer object>, mouse_callbacks=<function mouse_press_callbacks>, event=<ReadOnlyWrapper at 0x7f0c01647040 for MouseEvent>)
   1154 # Put a read only wrapper on the event
   1155 event = ReadOnlyWrapper(event, exceptions=('handled',))
-> 1156 mouse_callbacks(self.viewer, event)
        event = <ReadOnlyWrapper at 0x7f0c01647040 for MouseEvent at 0x7f0c288d1ed0>
        mouse_callbacks = <function mouse_press_callbacks at 0x7f0c89d52cb0>
        self.viewer = Viewer(camera=Camera(center=(0.0, 314.5, 314.5), zoom=1.019353960150897, angles=(0.0, 0.0, 90.0), perspective=0.0, mouse_pan=True, mouse_zoom=True), cursor=Cursor(position=(91.0, 763.3136607686552, 462.14252269423287), scaled=True, size=10, style=<CursorStyle.STANDARD: 'standard'>), dims=Dims(ndim=3, ndisplay=2, last_used=0, range=((0.0, 184.0, 1.0), (0.0, 630.0, 1.0), (0.0, 630.0, 1.0)), current_step=(91, 314, 314), order=(0, 1, 2), axis_labels=('0', '1', '2')), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layers=[<Image layer '...ddings/TS_1_1/TS_1_1_noctf.mrc' at 0x7f0c2a582e00>, <Labels layer 'UMAP' at 0x7f0b19471ff0>], help='use <1> for activate the label eraser, use <2> for activate the paint brush, use <3> for activate the fill bucket, use <4> for pick mode', status={'layer_base': 'UMAP', 'source_type': '', 'plugin': '', 'coordinates': ' [91 763 462]'}, tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_over_canvas=True, mouse_move_callbacks=[], mouse_drag_callbacks=[functools.partial(<function drag_circle_callback at 0x7f0c2a5563b0>, <napari_clusters_plotter._plotter.PlotterWidget object at 0x7f0c2875e560>)], mouse_double_click_callbacks=[], mouse_wheel_callbacks=[<function dims_scroll at 0x7f0c88d2a170>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keymap={})
        self = <napari._qt.qt_viewer.QtViewer object at 0x7f0c800a2b90>
   1158 layer = self.viewer.layers.selection.active
   1159 if layer is not None:

File /hpc/projects/group.czii/saugat.kandel/miniforge3/envs/napari-tomotwin/lib/python3.10/site-packages/napari/utils/interactions.py:121, in mouse_press_callbacks(obj=Viewer(camera=Camera(center=(0.0, 314.5, 314.5),...ouse_drag_gen={}, _mouse_wheel_gen={}, keymap={}), event=<ReadOnlyWrapper at 0x7f0c01647040 for MouseEvent>)
    118 # iterate through drag callback functions
    119 for mouse_drag_func in obj.mouse_drag_callbacks:
    120     # execute function to run press event code
--> 121     gen = mouse_drag_func(obj, event)
        mouse_drag_func = functools.partial(<function drag_circle_callback at 0x7f0c2a5563b0>, <napari_clusters_plotter._plotter.PlotterWidget object at 0x7f0c2875e560>)
        obj = Viewer(camera=Camera(center=(0.0, 314.5, 314.5), zoom=1.019353960150897, angles=(0.0, 0.0, 90.0), perspective=0.0, mouse_pan=True, mouse_zoom=True), cursor=Cursor(position=(91.0, 763.3136607686552, 462.14252269423287), scaled=True, size=10, style=<CursorStyle.STANDARD: 'standard'>), dims=Dims(ndim=3, ndisplay=2, last_used=0, range=((0.0, 184.0, 1.0), (0.0, 630.0, 1.0), (0.0, 630.0, 1.0)), current_step=(91, 314, 314), order=(0, 1, 2), axis_labels=('0', '1', '2')), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layers=[<Image layer '...ddings/TS_1_1/TS_1_1_noctf.mrc' at 0x7f0c2a582e00>, <Labels layer 'UMAP' at 0x7f0b19471ff0>], help='use <1> for activate the label eraser, use <2> for activate the paint brush, use <3> for activate the fill bucket, use <4> for pick mode', status={'layer_base': 'UMAP', 'source_type': '', 'plugin': '', 'coordinates': ' [91 763 462]'}, tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_over_canvas=True, mouse_move_callbacks=[], mouse_drag_callbacks=[functools.partial(<function drag_circle_callback at 0x7f0c2a5563b0>, <napari_clusters_plotter._plotter.PlotterWidget object at 0x7f0c2875e560>)], mouse_double_click_callbacks=[], mouse_wheel_callbacks=[<function dims_scroll at 0x7f0c88d2a170>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keymap={})
        event = <ReadOnlyWrapper at 0x7f0c01647040 for MouseEvent at 0x7f0c288d1ed0>
    122     # if function returns a generator then try to iterate it
    123     if inspect.isgenerator(gen):

File ~/.local/lib/python3.10/site-packages/napari_tomotwin/anchor_tool.py:50, in drag_circle_callback(plotter_widget=<napari_clusters_plotter._plotter.PlotterWidget object>, viewer=Viewer(camera=Camera(center=(0.0, 314.5, 314.5),...ouse_drag_gen={}, _mouse_wheel_gen={}, keymap={}), event=<ReadOnlyWrapper at 0x7f0c01647040 for MouseEvent>)
     49 def drag_circle_callback(plotter_widget, viewer, event):
---> 50     data_coordinates = plotter_widget.layer_select.value.world_to_data(
        plotter_widget = <napari_clusters_plotter._plotter.PlotterWidget object at 0x7f0c2875e560>
        event = <ReadOnlyWrapper at 0x7f0c01647040 for MouseEvent at 0x7f0c288d1ed0>
     51         event.position
     52     )
     53     _draw_circle(
     54         plotter_widget,
     55         data_coordinates,
     56         plotter_widget.layer_select.value,
     57         plotter_widget.layer_select.value.features,
     58     )

AttributeError: 'PlotterWidget' object has no attribute 'layer_select'

Do you have any suggestions on how to resolve this?

[thorstenwagner]

Thanks for getting in touch :-) Will try to reproduce and fix it. Can you share the tomo+embedding+umap?

[saugatkandel]

I just tried this with the example data from the tutorial, and I still get the same problem. This is with my following exactly the steps from the tutorial, starting from the installation.

[thorstenwagner]

Thanks! Did the installation recently and everything worked fine. Will try to reproduce it though. 23.05.2024 20:57:20 saugatkandel ***@***.***>:

…

I just tried this with the example data from the tutorial, and I still get the same problem. This is with my following exactly the steps from the tutorial, starting from the installation. — Reply to this email directly, view it on GitHub[#33 (comment)], or unsubscribe[https://github.com/notifications/unsubscribe-auth/AAIP66PNDJDTKQSRQ6OGLF3ZDY3Y5AVCNFSM6AAAAABIEGXGWOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMRXHAZTGOJXHA]. You are receiving this because you commented. [Verfolgungsbild][https://github.com/notifications/beacon/AAIP66JIF42W6BSALUJQJQ3ZDY3Y5A5CNFSM6AAAAABIEGXGWOWGG33NNVSW45C7OR4XAZNMJFZXG5LFINXW23LFNZ2KUY3PNVWWK3TUL5UWJTT62QVXU.gif]

[saugatkandel]

This is my conda environment requirements:

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
anyio                     4.3.0              pyhd8ed1ab_0    conda-forge
archspec                  0.2.3              pyhd8ed1ab_0    conda-forge
argon2-cffi               23.1.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0          py310h2372a71_4    conda-forge
arrow                     1.3.0              pyhd8ed1ab_0    conda-forge
asttokens                 2.4.1              pyhd8ed1ab_0    conda-forge
async-lru                 2.0.4              pyhd8ed1ab_0    conda-forge
attrs                     23.2.0             pyh71513ae_0    conda-forge
babel                     2.14.0             pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.12.3             pyha770c72_0    conda-forge
bleach                    6.1.0              pyhd8ed1ab_0    conda-forge
boltons                   23.1.1             pyhd8ed1ab_0    conda-forge
brotli-python             1.1.0           py310hc6cd4ac_1    conda-forge
bzip2                     1.0.8                hd590300_5    conda-forge
c-ares                    1.27.0               hd590300_0    conda-forge
ca-certificates           2024.2.2             hbcca054_0    conda-forge
cached-property           1.5.2                hd8ed1ab_1    conda-forge
cached_property           1.5.2              pyha770c72_1    conda-forge
certifi                   2024.2.2           pyhd8ed1ab_0    conda-forge
cffi                      1.16.0          py310h2fee648_0    conda-forge
charset-normalizer        3.3.2              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
comm                      0.2.2              pyhd8ed1ab_0    conda-forge
conda                     24.1.2          py310hff52083_0    conda-forge
conda-libmamba-solver     24.1.0             pyhd8ed1ab_0    conda-forge
conda-package-handling    2.2.0              pyh38be061_0    conda-forge
conda-package-streaming   0.9.0              pyhd8ed1ab_0    conda-forge
debugpy                   1.8.1           py310hc6cd4ac_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
distro                    1.9.0              pyhd8ed1ab_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
exceptiongroup            1.2.0              pyhd8ed1ab_2    conda-forge
executing                 2.0.1              pyhd8ed1ab_0    conda-forge
filelock                  3.13.4                   pypi_0    pypi
fmt                       10.2.1               h00ab1b0_0    conda-forge
fqdn                      1.5.1              pyhd8ed1ab_0    conda-forge
gdown                     5.1.0                    pypi_0    pypi
h11                       0.14.0             pyhd8ed1ab_0    conda-forge
h2                        4.1.0              pyhd8ed1ab_0    conda-forge
hpack                     4.0.0              pyh9f0ad1d_0    conda-forge
httpcore                  1.0.5              pyhd8ed1ab_0    conda-forge
httpx                     0.27.0             pyhd8ed1ab_0    conda-forge
hyperframe                6.0.1              pyhd8ed1ab_0    conda-forge
icu                       73.2                 h59595ed_0    conda-forge
idna                      3.6                pyhd8ed1ab_0    conda-forge
importlib-metadata        7.1.0              pyha770c72_0    conda-forge
importlib_metadata        7.1.0                hd8ed1ab_0    conda-forge
importlib_resources       6.4.0              pyhd8ed1ab_0    conda-forge
ipykernel                 6.29.3             pyhd33586a_0    conda-forge
ipython                   8.22.2             pyh707e725_0    conda-forge
isoduration               20.11.0            pyhd8ed1ab_0    conda-forge
jedi                      0.19.1             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.3              pyhd8ed1ab_0    conda-forge
json5                     0.9.24             pyhd8ed1ab_0    conda-forge
jsonpatch                 1.33               pyhd8ed1ab_0    conda-forge
jsonpointer               2.4             py310hff52083_3    conda-forge
jsonschema                4.21.1             pyhd8ed1ab_0    conda-forge
jsonschema-specifications 2023.12.1          pyhd8ed1ab_0    conda-forge
jsonschema-with-format-nongpl 4.21.1             pyhd8ed1ab_0    conda-forge
jupyter-lsp               2.2.5              pyhd8ed1ab_0    conda-forge
jupyter_client            8.6.1              pyhd8ed1ab_0    conda-forge
jupyter_core              5.7.2           py310hff52083_0    conda-forge
jupyter_events            0.10.0             pyhd8ed1ab_0    conda-forge
jupyter_server            2.13.0             pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.5.3              pyhd8ed1ab_0    conda-forge
jupyterlab                4.1.6              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.3.0              pyhd8ed1ab_1    conda-forge
jupyterlab_server         2.26.0             pyhd8ed1ab_0    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
krb5                      1.21.2               h659d440_0    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
libarchive                3.7.2                h2aa1ff5_1    conda-forge
libcurl                   8.6.0                hca28451_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 hd590300_2    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.2.0               h807b86a_5    conda-forge
libgomp                   13.2.0               h807b86a_5    conda-forge
libiconv                  1.17                 hd590300_2    conda-forge
libmamba                  1.5.7                had39da4_0    conda-forge
libmambapy                1.5.7           py310h39ff949_0    conda-forge
libnghttp2                1.58.0               h47da74e_1    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsolv                   0.7.28               hfc55251_0    conda-forge
libsqlite                 3.45.2               h2797004_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-ng              13.2.0               h7e041cc_5    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libxml2                   2.12.6               h232c23b_0    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
lz4-c                     1.9.4                hcb278e6_0    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
mamba                     1.5.7           py310h51d5547_0    conda-forge
markupsafe                2.1.5           py310h2372a71_0    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
menuinst                  2.0.2           py310hff52083_0    conda-forge
mistune                   3.0.2              pyhd8ed1ab_0    conda-forge
nbclient                  0.10.0             pyhd8ed1ab_0    conda-forge
nbconvert-core            7.16.3             pyhd8ed1ab_1    conda-forge
nbformat                  5.10.4             pyhd8ed1ab_0    conda-forge
ncurses                   6.4.20240210         h59595ed_0    conda-forge
nest-asyncio              1.6.0              pyhd8ed1ab_0    conda-forge
notebook-shim             0.2.4              pyhd8ed1ab_0    conda-forge
openssl                   3.2.1                hd590300_1    conda-forge
overrides                 7.7.0              pyhd8ed1ab_0    conda-forge
packaging                 24.0               pyhd8ed1ab_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parso                     0.8.4              pyhd8ed1ab_0    conda-forge
pexpect                   4.9.0              pyhd8ed1ab_0    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pip                       24.0               pyhd8ed1ab_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_1    conda-forge
platformdirs              4.2.0              pyhd8ed1ab_0    conda-forge
pluggy                    1.4.0              pyhd8ed1ab_0    conda-forge
prometheus_client         0.20.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.42             pyha770c72_0    conda-forge
psutil                    5.9.8           py310h2372a71_0    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pybind11-abi              4                    hd8ed1ab_3    conda-forge
pycosat                   0.6.6           py310h2372a71_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.17.2             pyhd8ed1ab_0    conda-forge
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.10.14         hd12c33a_0_cpython    conda-forge
python-dateutil           2.9.0              pyhd8ed1ab_0    conda-forge
python-fastjsonschema     2.19.1             pyhd8ed1ab_0    conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python_abi                3.10                    4_cp310    conda-forge
pytz                      2024.1             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0.1           py310h2372a71_1    conda-forge
pyzmq                     25.1.2          py310h795f18f_0    conda-forge
readline                  8.2                  h8228510_1    conda-forge
referencing               0.34.0             pyhd8ed1ab_0    conda-forge
reproc                    14.2.4.post0         hd590300_1    conda-forge
reproc-cpp                14.2.4.post0         h59595ed_1    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rpds-py                   0.18.0          py310hcb5633a_0    conda-forge
ruamel.yaml               0.18.6          py310h2372a71_0    conda-forge
ruamel.yaml.clib          0.2.8           py310h2372a71_0    conda-forge
send2trash                1.8.3              pyh0d859eb_0    conda-forge
setuptools                69.2.0             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sniffio                   1.3.1              pyhd8ed1ab_0    conda-forge
soupsieve                 2.5                pyhd8ed1ab_1    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
terminado                 0.18.1             pyh0d859eb_0    conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tornado                   6.4             py310h2372a71_0    conda-forge
tqdm                      4.66.2             pyhd8ed1ab_0    conda-forge
traitlets                 5.14.2             pyhd8ed1ab_0    conda-forge
truststore                0.8.0              pyhd8ed1ab_0    conda-forge
types-python-dateutil     2.9.0.20240316     pyhd8ed1ab_0    conda-forge
typing-extensions         4.11.0               hd8ed1ab_0    conda-forge
typing_extensions         4.11.0             pyha770c72_0    conda-forge
typing_utils              0.1.0              pyhd8ed1ab_0    conda-forge
tzdata                    2024a                h0c530f3_0    conda-forge
uri-template              1.3.0              pyhd8ed1ab_0    conda-forge
urllib3                   2.2.1              pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.13             pyhd8ed1ab_0    conda-forge
webcolors                 1.13               pyhd8ed1ab_0    conda-forge
webencodings              0.5.1              pyhd8ed1ab_2    conda-forge
websocket-client          1.7.0              pyhd8ed1ab_0    conda-forge
wheel                     0.43.0             pyhd8ed1ab_0    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
yaml-cpp                  0.8.0                h59595ed_0    conda-forge
zeromq                    4.3.5                h59595ed_1    conda-forge
zipp                      3.17.0             pyhd8ed1ab_0    conda-forge
zstandard                 0.22.0          py310h1275a96_0    conda-forge
zstd                      1.5.5                hfc55251_0    conda-forge

The linux version is:

Linux 4.18.0-513.18.1.el8_9.x86_64 x86_64

LSB Version:	:core-4.1-amd64:core-4.1-noarch:cxx-4.1-amd64:cxx-4.1-noarch:desktop-4.1-amd64:desktop-4.1-noarch:languages-4.1-amd64:languages-4.1-noarch:printing-4.1-amd64:printing-4.1-noarch
Distributor ID:	Rocky
Description:	Rocky Linux release 8.9 (Green Obsidian)
Release:	8.9
Codename:	GreenObsidian

[thorstenwagner]

Hey! The environment you posted has no napari installed. Is it maybe your base environment? Anyway, I just released a couple of fixes for the installation.

Can you run the following commands and try again?

mamba env remove -n napari-tomotwin
mamba env create -n napari-tomotwin -f https://raw.githubusercontent.com/MPI-Dortmund/napari-tomotwin/main/conda_env.yml
conda activate napari-tomotwin
pip install napari-tomotwin