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Activity
    Jan C. Frankowski
    @janfpl
    I'm getting a message to upgrade brainio 0.0.11 to 0.0.12 in amap and cellfinder. When I run pip install brainio --upgrade, it says I have 0.012 installed, but I keep getting the messages to upgrade. I'm also getting FileNotFoundErrors when I try to run registration that ran successfully about a month ago. Any idea if these are related?
    Adam Tyson
    @adamltyson
    Hi, you can ignore the brainio message, that’s a bug that I need to sort out.
    Adam Tyson
    @adamltyson
    About the other error, have you updated amap since the successful registration? Could you send me the log files of both (successful and not) attempts?
    Jun
    @Jun-Lizst
    Hi. I just find out cellfinder will be useful. trying recently.
    sthitapati
    @sthitapati

    Hi Adam! I have a couple of errors during visualization.
    (1) While running
    amap_vis "C:\Users\sthit\Documents\rabies_D2_ToS\out\registration" or cellfinder_region_summary "C:\Users\sthit\Documents\rabies_D2_ToS\out\registration"

    File "c:\users\sthit\anaconda3\envs\cellfinder\lib\site-packages\imlib\source\source_files.py", line 29, in get_structures_path
    atlas_conf = config_obj["atlas"]
    File "c:\users\sthit\anaconda3\envs\cellfinder\lib\site-packages\configobj.py", line 554, in getitem
    val = dict.getitem(self, key)
    KeyError: 'atlas'

    (2) While trying to save all layers from cellfinder visualizer,

    File "c:\users\sthit\anaconda3\envs\cellfinder\lib\site-packages\napari\plugins\io.py", line 273, in _write_multiple_layers_with_plugins
    raise PluginCallError(implementation, cause=exc)
    napari_plugin_engine.exceptions.PluginCallError: Error in plugin 'builtins', hook 'napari_get_writer': Error in plugin 'builtins', hook 'napari_write_image'

    Adam Tyson
    @adamltyson
    Sorry about this.
    13 replies
    For number (2), this is a feature in napari that isn't yet supported by cellfinder
    Jun
    @Jun-Lizst
    Are there some tutorial videos?
    Adam Tyson
    @adamltyson

    Are there some tutorial videos?

    Nothing yet, sorry. There is some improved documentation, but cellfinder is nowhere near finished, so unfortunately it's unlikely that there will be any tutorials etc. for a while.

    Jun
    @Jun-Lizst
    well. thanks
    Chouchi974
    @Chouchi974
    hi!
    I have a problem to visualise results. It say that the command cellfinder_view doesn't exist. Do it mean that my cellfinder isn't update ? how can i uptade it ?
    5 replies
    Adam Tyson
    @adamltyson
    Sorry, could you try pip install neuro —upgrade?
    Chouchi974
    @Chouchi974

    (cellfinder) C:\Users\guill>pip install neuro-upgrade
    ERROR: Could not find a version that satisfies the requirement neuro-upgrade (from versions: none)
    ERROR: No matching distribution found for neuro-upgrade

    Nothing happened after this command

    6 replies
    Chouchi974
    @Chouchi974
    cellfinder_2020-06-17_14-45-45.log
    1 reply
    Hi. I have another issue. When I want cellfinder to generate figure and summarise, it starts the registration but it stops and says that affine registration failed. here are the log :
    What should I do ? Where did I made a mistake ? thanks for your help
    Chouchi974
    @Chouchi974
    affine.err
    1 reply
    there's this one
    and the other one is empty
    Jan C. Frankowski
    @janfpl
    Hi! I am trying to register a light sheet scan of a whole mouse brain using amap with the default parameters. The registration performs reasonably well, but there seems to be consistent mismatch between the borders of the tissue and the outside edges of the atlas. Any tips on how to more accurately align the edges? Our protocol has steps to reduce tissue autofluorescence so the signal:noise is very poor - background is around ~200 while signal ranges between 250-450 with a 16-bit histogram
    12 replies
    amap.PNG
    Adam Tyson
    @adamltyson
    I didn’t mean measure it, if you view it overlaid on top of the downsampled.nii file, you can see if it’s scaled appropriately.
    Jan C. Frankowski
    @janfpl
    So this would show the boundaries before the freeform transformation? I'm not familiar with how to work with .nii files, is there a way to do this with cellfinder/amap?
    Adam Tyson
    @adamltyson
    This will show the registered data itself (ie the atlas template image warped to your data). You should be able to open the nii image in FIJI or in Napari with the right plugins (this will have been installed with amap).
    If you open the downsampled image, then overlay the affine registered image, you should see an image that’s roughly aligned with your data.
    The free form registered image will then be the properly (or not in your case) aligned image.
    If the affine image is of the right size, and roughly aligned with your brain, then the problem probably lies in the free form step.
    I’d like get this fixed though, so I’m happy to have a quick chat on zoom, or if you can send me some data I’ll take a look.
    Jan C. Frankowski
    @janfpl
    nii overlay.PNG
    The affine_registered_atlas_brain.nii (magenta) overlays fairly well over the downsampled image (green).
    I'll send you a link to the raw data privately. Thanks for your help!
    Adam Tyson
    @adamltyson
    Great, I'll take a look. That affine registration looks pretty good, so hopefully we can tweak the freeform step.
    Chouchi974
    @Chouchi974
    Hi !
    I have a problem regarding the training of the network.
    When I use the curation command, this line appears just after my command :
    WARNING: Cannot mix incompatible Qt library (version 0x50c03) with this library (version 0x50c09)
    Do you have any idea how to fix it ?
    Thanks for your help !
    6 replies
    Adam Tyson
    @adamltyson
    brainreg.png
    Hi @janfpl, I had a quick look at your data, and it seems like some of the registration problems might be due to the data itself (damage to the front of the brain, what looks like stitching artefacts, and some bright signal outside of the brain). I'll have a play around to see if I can improve it, but interestingly, using the 25um resolution atlas in brainreg (https://github.com/brainglobe/brainreg) seems to look a bit better than the image you sent (see above).
    It's still not great though.
    If you want to try out brainreg, this is the command I used:
    brainreg /path/to/data /path/to/output -x 3.6498 -y 3.6498 -z 15.3767 --orientation lsp --atlas allen_mouse_25um
    Jan C. Frankowski
    @janfpl
    Awesome! I’ll try it out and let you know how it works.
    adam-romanski
    @adam-romanski

    Hi!
    I am having a problem with registering a brain for a current project. Right before the Debug process starts to run I receive this error:

    Traceback (most recent call last):
    File "c:\users\administrator\miniconda3\envs\cellfinder\lib\concurrent\futures\process.py", line 239, in _process_worker
    r = call_item.fn(call_item.args, *call_item.kwargs)
    File "c:\users\administrator\miniconda3\envs\cellfinder\lib\site-packages\brainio\brainio.py", line 465, in load_from_paths_sequence
    return volume
    UnboundLocalError: local variable 'volume' referenced before assignment

    This error only occurs with this one brain. All other brains I register succeed. Thank you for your help!