I am trying the various models and having some success with initial segmentation, especially when i first denoise my tomograms with the easymode denoise. I have run into an issue with the mitochondrion model which is part of the list of models:
$ easymode list
easymode can currently segment the following features:
> actin 3D/2D (default: 3D)
> cytoplasm 2D
> cytoplasmic_granule 3D
> ferritin 2D
> hfimpdh 2D
> ice_particle 2D
> intermediate_filament 3D
> lipid_droplet 2D
> membrane 3D/2D (default: 3D)
> microtubule 3D/2D (default: 3D)
> mitochondrial_granule 3D
> mitochondrion 2D
> npc 3D/2D (default: 3D)
> nuclear_envelope 2D
> nucleus 2D
> prohibitin 3D
> proteasome 2D
> ribosome 3D/2D (default: 3D)
> tric 3D
> vault 3D
> void 3D/2D (default: 3D)
When running the command, here's the output:
$ easymode segment mitochondrion --data ./ --apix 9 --gpu 3
mitochondrion: using 3D model
easymode segment
feature: mitochondrion
data_patterns: ['./']
output_directory: segmented
output_format: int8
gpus: [3]
tta: 4
overwrite: False
batch_size: 1
Found 1 tomograms to segment.
Model 'mitochondrion' not found. For an up-to-date list of available models, run 'easymode list'
Could not find model for mitochondrion! Exiting.
I am trying the various models and having some success with initial segmentation, especially when i first denoise my tomograms with the easymode denoise. I have run into an issue with the mitochondrion model which is part of the list of models:
When running the command, here's the output: