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chenhungling / CaimanGUI

GUI for visualizing CaImAn processed imaging data.
GNU General Public License v3.0
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3D data #1

Open rajlakshmi-sawale opened 1 month ago

rajlakshmi-sawale commented 1 month ago

Hi @chenhungling, Does the GUI work on 3D data? I have 3D data and I'm getting this error when I try to load it: Can we solve this?

(caiman) C:\Users\au711234\CaimanGUI\gui>python caiman_gui.py
Traceback (most recent call last):
  File "C:\Users\au711234\CaimanGUI\gui\caiman_gui.py", line 126, in <lambda>
    openHDF5.triggered.connect(lambda: self.load_data(click=True))
  File "C:\Users\au711234\CaimanGUI\gui\caiman_gui.py", line 243, in load_data
    img_components = [A[:,i].reshape(dims,order='F').toarray() for i in range(A.shape[1])]
  File "C:\Users\au711234\CaimanGUI\gui\caiman_gui.py", line 243, in <listcomp>
    img_components = [A[:,i].reshape(dims,order='F').toarray() for i in range(A.shape[1])]
  File "C:\ProgramData\Anaconda3\envs\caiman\lib\site-packages\scipy\sparse\_base.py", line 161, in reshape
    shape = check_shape(args, self.shape, allow_1d=is_array)
  File "C:\ProgramData\Anaconda3\envs\caiman\lib\site-packages\scipy\sparse\_sputils.py", line 362, in check_shape
    raise ValueError('matrix shape must be two-dimensional')
ValueError: matrix shape must be two-dimensional
chenhungling commented 1 week ago

Hi Rajlakshmi,

Sorry that our GUI was not designed to take 3D data but rather focused on time series of single plane data. If you have only a few planes with no overlapping cells, you can always split the planes and treat them independently.

Best regards, Hung-Ling

On Wed, Aug 14, 2024 at 4:02 PM Rajlakshmi Sawale @.***> wrote:

Hi @chenhungling https://github.com/chenhungling, Does the GUI work on 3D data? I have 3D data and I'm getting this error when I try to load it: Can we solve this?

(caiman) C:\Users\au711234\CaimanGUI\gui>python caiman_gui.py Traceback (most recent call last): File "C:\Users\au711234\CaimanGUI\gui\caiman_gui.py", line 126, in openHDF5.triggered.connect(lambda: self.load_data(click=True)) File "C:\Users\au711234\CaimanGUI\gui\caiman_gui.py", line 243, in load_data img_components = [A[:,i].reshape(dims,order='F').toarray() for i in range(A.shape[1])] File "C:\Users\au711234\CaimanGUI\gui\caiman_gui.py", line 243, in img_components = [A[:,i].reshape(dims,order='F').toarray() for i in range(A.shape[1])] File "C:\ProgramData\Anaconda3\envs\caiman\lib\site-packages\scipy\sparse_base.py", line 161, in reshape shape = check_shape(args, self.shape, allow_1d=is_array) File "C:\ProgramData\Anaconda3\envs\caiman\lib\site-packages\scipy\sparse_sputils.py", line 362, in check_shape raise ValueError('matrix shape must be two-dimensional') ValueError: matrix shape must be two-dimensional

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