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aelefebv / nellie

Nellie: Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy
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type object 'XmlSerializer' has no attribute 'encode' #16

Closed Amirhk-dev closed 3 months ago

Amirhk-dev commented 3 months ago

Hi, I have installed "Nellie" via the Napari plugin manager. It is possible to select and visualize the file "yeast_3d_mitochondria.ome.tif" but clicking "Run preprocessing" generates the "type object 'XmlSerializer' has no attribute 'encode'" error.

How is it possible to resolve this issue?

Below is part of the Traceback:

AttributeError Traceback (most recent call last) File /opt/anaconda3/envs/nellie_env/lib/python3.11/site-packages/nellie_napari/nellie_processor.py:186, in NellieProcessor.run_preprocessing(self=) 183 def run_preprocessing(self): 184 preprocessing = Filter(im_info=self.nellie.im_info, num_t=self.num_t, 185 remove_edges=self.remove_edges_checkbox.isChecked()) --> 186 preprocessing.run() preprocessing = <nellie.segmentation.filtering.Filter object at 0x2d8ae6150> 188 self.check_file_existence()

Thanks.

aelefebv commented 3 months ago

Hi Amir, weird I haven't seen this error before. Can you send the file to austin.e.lefebvre@gmail.com if possible? I'll take a look.

Amirhk-dev commented 3 months ago

Hi Austin, I just sent the email. Thank you.