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denisecailab / minian

miniscope analysis pipeline with interactive visualizations
GNU General Public License v3.0
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Rings in Video #275

Open kaylanguyen1 opened 1 month ago

kaylanguyen1 commented 1 month ago

Hello,

We are currently using the Minian pipeline to process a .tiff video file about 30 minutes long. We tested some .avi sample videos which have a similar appearance to the videos in the training video, but the .tiff file has concentric rings throughout the video, despite the absence of such artifacts in the raw footage. Is this an issue with the video file or file type, or is there a way to remove these rings to achieve a smoother appearance to better show the visible cells? In addition, will these rings have an effect on the C-trace visualization?

Thank you in advance for any advice or answers!

Attached is a frame from a previous .avi file, then the .tiff file we just ran through the pipeline.

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austinbaggetta commented 1 month ago

Hi! Can you share what your .tiff file looks like? Or could you share the file with me so I can take a look? I haven't seen anything like this before unfortunately.

kaylanguyen1 commented 1 month ago

Hi! Can you share what your .tiff file looks like? Or could you share the file with me so I can take a look? I haven't seen anything like this before unfortunately.

Unfortunately, the file is too big to post but here's a frame from the video. I didn't change anything in the pipeline other than replacing the .avi file with a .tiff file and increasing the worker count and memory. b65bebf4-1c80-4f30-b265-6971c8cf16fe

austinbaggetta commented 1 month ago

Can you share your pre-processing parameters and code up until the first saving step? The parameters specifically for glow removal, denoising, and background removal. In the image you showed you can see faint concentric rings, which the background parameters may be highlighting. Without seeing the full video it's hard to say, but I believe these concentric rings can become highlighted when there is poor signal to noise during the imaging.

kaylanguyen1 commented 1 month ago

Can you share your pre-processing parameters and code up until the first saving step? The parameters specifically for glow removal, denoising, and background removal. In the image you showed you can see faint concentric rings, which the background parameters may be highlighting. Without seeing the full video it's hard to say, but I believe these concentric rings can become highlighted when there is poor signal to noise during the imaging.

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