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Polus cellpose inference plugin#14
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Nicholas-Schaub wants to merge 47 commits intoPolusAI:masterfrom
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hsidky
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Jul 21, 2021
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Looks good. Just a few minor adjustments to the readme mainly to bring it into consistency with the plugin.
| tile_img = br[y_min:y_max, x_min:x_max, z:z + 1, 0, 0].squeeze() | ||
| img = cellpose.transforms.convert_image(tile_img,[0,0],False,True,False) | ||
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| if diameter in [None,0]: |
| bw.dtype = np.float32 | ||
| bw.channel_names = ['cell_probability','x','y','labels'] | ||
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| bw._backend._init_writer() |
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Why is it necessary to call the backend? Would be useful to know why this programming pattern was used with biowriter
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| | Name | Description | I/O | Type | | ||
| |---------------|-------------------------|--------|--------| | ||
| | `--diameter` | Diameter| Input | number | |
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diameterMode and and filePattern missing, while cpretrainedModel is not in the plugin json manifest.
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This PR updates the cellpose inference plugin to run using the Cellpose package. The previous iteration of the plugin used bits and pieces of an older version of Cellpose. Cellpose has since had multiple commits and upgrades, and trying to incorporate those commits into a custom codebase will be difficult in the long run.
This PR also resolves some issues when trying to run the container as a user.