Comments (6)
Right, when I open the denoised.tif in imageJ it shows all the frames. The code should be all good, thank you very much! Maybe I need to find another way to load it on python, the denoised.tif 's 32-bit format may cause cv2's problem I guess anyway.
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I tried to use python's cv2.imread(denoised.tif,-1) to read the output tiff file, it seems the result is only one image instead of a whole 3-D movie. I checked the testGUI.py is using tifffile.imwrite(append = 'True'), so I don't know what's wrong with it?
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In our side, we're not sure if that issue exist... With test_GUI, I checked that denoised.tif contains multiple frames, not only one frame.
Did you tried with demo data at src/sample_data.tif
??
I just tried as followings.
python -m src.GUI.test_GUI
to open GUI.- Browse src/sample_data.tif. Then, start index will be 1 and end index will be displayed as 300. Also, save path will be automatically selected as
data/SUPPORT/current_timestamp/
. - Press Run button. And if you go to the save path, you may see the size of
denoised.tif
will keep increasing as the inference goes on. I'm not sure of cv2.imread, but if I open thedenoised.tif
with ImageJ/fiji, the data contains 300 frames.
If you did not tried with demo data, please check if our code with this data works well.
Let me know if it works or not.
Also, if the code with demo data works well, but not for your custom data, let me know. We can find if the code is going wrong with your data.
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Ah okay, I also do not use cv2 when dealing with these microscopy images (I feel like they are well suited to 8bit "natural" images).
I think tifffile package or skimage.io package will be nice to load 16 or 32-bit images.
(Internally, skimage.io will use tifffile to read and write with tif images)
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Right, when I open the denoised.tif in imageJ it shows all the frames. The code should be all good, thank you very much! Maybe I need to find another way to load it on python, the denoised.tif 's 32-bit format may cause cv2's problem I guess anyway.
Hi! May I ask if you resolved the problem already? I tried skimage.io but it still only gives one frame image. I checked the metadata in ImageJ, the problem seems to be a wrong dimension (the T dimension was written as the Z dimension).
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Related Issues (7)
- Is env.yml file missing? HOT 4
- Could not load the Qt platform plugin "xcb" in "" even though it was found. HOT 1
- Train GUI missing is_rotate HOT 1
- src.test RuntimeError: Error(s) in loading state_dict for SUPPORT: HOT 1
- PyQt5 import issue when running the GUI HOT 15
- Model used in the publication HOT 27
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