Hello Francois,
I'm Fumihiro, who was in the Antoine Triller's lab and I want to use TRamWAy for single particle tracking analysis.
Describe the bug
When I try to visualize TRamWAy results (RWA file) with the Bokeh-based viewer, the browser tab opens at http://localhost:5006/... and the console prints “Bokeh items were rendered successfully”, but the page itself is completely blank (no plots or widgets are shown).
To Reproduce
Steps to reproduce the behavior:
Activate the tramway_env conda environment.
Launch a Jupyter notebook on Windows and run a TRamWAy tutorial / example that opens the Bokeh viewer (e.g. ... – fill in the exact script or notebook cell you used).
Wait for the browser to open at the Bokeh server URL (e.g. http://localhost:5006/...).
Observe that the page remains entirely blank, even though there are no visible Python errors.
Expected behavior
The Bokeh viewer should display the TRamWAy GUI (plots and controls) in the browser window instead of an empty page.
A screenshot of the blank browser page.
Console
text
[Bokeh] setting log level to: 'info'
Bokeh items were rendered successfully
WebSocket connection to 'ws://localhost:5006/...' was opened
If there are any error messages in the JS console or the Python terminal, please paste them here inside triple backticks as well.
System
Operating System: Windows 11 x64
Python version: 3.10.19 | packaged by Anaconda, Inc. | (main, Oct 21 2025, 16:41:31) [MSC v.1929 64 bit (AMD64)]
TRamWAy version: 0.6.9
NumPy version: 1.24.3
Bokeh version: 2.4.3
Tornado version: 6.1
Selenium version: 4.40.0
Additional context
I checked the existing TRamWAy issue related to Bokeh (e.g. #44), but my symptoms are different: in my case, the Bokeh server starts and reports successful rendering, yet the browser remains completely blank (no visible content).
The WebSocket connection appears to succeed in the browser console.
This behavior is reproducible across multiple runs and persists after restarting Jupyter / the browser (Edge, Chrome, Firefox).
What I am asking
Is the Bokeh viewer (via RWAnalyzer.browser.show_maps) known to work with a specific range of versions (Bokeh, Tornado, NumPy, etc.)?
If so, which versions would you recommend for a Windows 11 / Anaconda environment?
For a .rwa file with the structure above, what is the intended/official way to access the spatial coordinates corresponding to a Maps object like 'dv d=20 v=1 j=1'?
In particular, how can I obtain the cell-centre positions (or polygons) that match the rows of maps_obj.maps, so that I can reconstruct the potential map manually with Matplotlib if the Bokeh viewer cannot be made to work?
Is there any known reason why a.browser.show_maps(...) might produce a completely blank page (no layout, no widgets, but with “Bokeh items were rendered successfully” in the console) under Bokeh 2.4.3, and if so, is there a recommended workaround?
Any guidance on a known-good environment (exact versions) and on how to correctly retrieve the spatial geometry (cell centres) from this kind of .rwa would be very helpful.
Hello Francois,
I'm Fumihiro, who was in the Antoine Triller's lab and I want to use TRamWAy for single particle tracking analysis.
Describe the bug
When I try to visualize TRamWAy results (RWA file) with the Bokeh-based viewer, the browser tab opens at http://localhost:5006/... and the console prints “Bokeh items were rendered successfully”, but the page itself is completely blank (no plots or widgets are shown).
To Reproduce
Steps to reproduce the behavior:
Activate the tramway_env conda environment.
Launch a Jupyter notebook on Windows and run a TRamWAy tutorial / example that opens the Bokeh viewer (e.g. ... – fill in the exact script or notebook cell you used).
Wait for the browser to open at the Bokeh server URL (e.g. http://localhost:5006/...).
Observe that the page remains entirely blank, even though there are no visible Python errors.
Expected behavior
The Bokeh viewer should display the TRamWAy GUI (plots and controls) in the browser window instead of an empty page.
A screenshot of the blank browser page.
Console
text
[Bokeh] setting log level to: 'info'
Bokeh items were rendered successfully
WebSocket connection to 'ws://localhost:5006/...' was opened
If there are any error messages in the JS console or the Python terminal, please paste them here inside triple backticks as well.
System
Operating System: Windows 11 x64
Python version: 3.10.19 | packaged by Anaconda, Inc. | (main, Oct 21 2025, 16:41:31) [MSC v.1929 64 bit (AMD64)]
TRamWAy version: 0.6.9
NumPy version: 1.24.3
Bokeh version: 2.4.3
Tornado version: 6.1
Selenium version: 4.40.0
Additional context
I checked the existing TRamWAy issue related to Bokeh (e.g. #44), but my symptoms are different: in my case, the Bokeh server starts and reports successful rendering, yet the browser remains completely blank (no visible content).
The WebSocket connection appears to succeed in the browser console.
This behavior is reproducible across multiple runs and persists after restarting Jupyter / the browser (Edge, Chrome, Firefox).
What I am asking
Is the Bokeh viewer (via RWAnalyzer.browser.show_maps) known to work with a specific range of versions (Bokeh, Tornado, NumPy, etc.)?
If so, which versions would you recommend for a Windows 11 / Anaconda environment?
For a .rwa file with the structure above, what is the intended/official way to access the spatial coordinates corresponding to a Maps object like 'dv d=20 v=1 j=1'?
In particular, how can I obtain the cell-centre positions (or polygons) that match the rows of maps_obj.maps, so that I can reconstruct the potential map manually with Matplotlib if the Bokeh viewer cannot be made to work?
Is there any known reason why a.browser.show_maps(...) might produce a completely blank page (no layout, no widgets, but with “Bokeh items were rendered successfully” in the console) under Bokeh 2.4.3, and if so, is there a recommended workaround?
Any guidance on a known-good environment (exact versions) and on how to correctly retrieve the spatial geometry (cell centres) from this kind of .rwa would be very helpful.