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    Jan C. Frankowski
    @janfpl
    Hi Adam,
    I'm trying out brainreg instead of using amap to register my mouse brain data. I inspected the overlay of the atlas boundaries and downsampled image using imageJ and it looks like the registration is more accurate. And it only took <4min instead of over 40min! Is there any way to inspect the results with napari?
    Adam Tyson
    @adamltyson
    I still need to make a proper viewer, but if you open napari, you should be able to just drag and drop the images.
    Set the boundaries images to “transparent” (or whatever it’s called) and you should see the overlay.
    Jan C. Frankowski
    @janfpl

    I recently upgraded to brainreg 0.1.1 from 0.0.3 and now I'm getting the following error:

    (cellfinder3) C:\Users\Workhorse>brainreg
    Traceback (most recent call last):
      File "c:\users\workhorse\anaconda3\envs\cellfinder3\lib\runpy.py", line 193, in _run_module_as_main
        "__main__", mod_spec)
      File "c:\users\workhorse\anaconda3\envs\cellfinder3\lib\runpy.py", line 85, in _run_code
        exec(code, run_globals)
      File "C:\Users\Workhorse\anaconda3\envs\cellfinder3\Scripts\brainreg.exe\__main__.py", line 4, in <module>
    ImportError: cannot import name 'main' from 'brainreg.cli' (c:\users\workhorse\anaconda3\envs\cellfinder3\lib\site-packages\brainreg\cli.py)

    If I revert back to 0.0.3, no more error messages. Do you know what would cause this issue?

    Adam Tyson
    @adamltyson
    My fault, can you try pip install brainreg --upgrade to update to 0.1.3, and this should be fixed.
    Adam Tyson
    @adamltyson
    FYI - there is now a small brainreg tutorial: https://docs.cellfinder.info/brainreg/tutorial
    lynettelim18
    @lynettelim18
    Hi is it possible to only register the coronal sections of the cortex and not the cerebellum?
    1 reply
    gongzhongyan
    @gongzhongyan
    Hi Adam, thank you for recommending the Brainreg. I got the sample data you had on the website running and I think it looks very promising to me. I wonder what are the requirements and parameters for the images if I want to process my own images? Are they need to be in the same size?
    8 replies
    mkunst23
    @mkunst23
    Hi, I'm having trouble installing brainreg. When I try to install I get the following error message: ERROR: Could not find a version that satisfies the requirement vtkplotter
    ERROR: No matching distribution found for vtkplotter So far I tried on a Mac and a Windows machine
    Adam Tyson
    @adamltyson
    Hey, can you try installing into a new conda environment? Brainreg doesn’t use vtkplotter, so it seems like that may be left behind by something else (maybe an old version of brainrender?).
    1 reply
    Also, brainreg is not tested on Mac, so it may not work properly.
    Adam Tyson
    @adamltyson
    It looks like vtkplotter has been totally removed from PyPI, causing this issue. could you raise an issue on the brainreg GitHub (I won’t have time to look at it until January though)?
    1 reply
    Justin Smith
    @smith6jt-cop
    Hello, I was getting good results several weeks ago, but tried recently and received a "ValueError: Supply a single scale, or one value per spatial axis" error. Do you know what could be causing this?
    13 replies
    Justin Smith
    @smith6jt-cop
    After running brainreg I am getting the following message trying to open napari:(envbrainreg2) C:\Users\smith6jt>napari
    c:\users\smith6jt\miniconda3\envs\envbrainreg2\lib\site-packages\qtpy__init__.py:215: RuntimeWarning: Selected binding "pyqt5" could not be found, using "pyside2"
    warnings.warn('Selected binding "{}" could not be found, '
    08:37:17 WARNING Could not import pyopencl. Falling back to scipy for CPU affine transforms
    Loading brainreg directory
    allen mouse atlas (res. 10um)
    From: http://www.brain-map.org (Wang et al 2020, https://doi.org/10.1016/j.cell.2020.04.007 )
    Adam Tyson
    @adamltyson
    Hi all. BrainGlobe has joined https://forum.image.sc as a community partner. Going forward, please ask any BrainGlobe questions over there, tagging brainglobe and the tool you're asking about, e.g. cellfinder. This Gitter channel will no longer be monitored. Thanks!