Stardist

[Mdack1]

Hi, I am trying to run the below from the standard workflow recieving this error. Please can you help?

b2c.stardist(image_path="stardist/he.tiff",
labels_npz_path="stardist/he.npz",
stardist_model="2D_versatile_he",
prob_thresh=0.1
)

Found model '2D_versatile_he' for 'StarDist2D'.

OSError Traceback (most recent call last)
Cell In[33], line 1
----> 1 b2c.stardist(image_path="stardist/he.tiff",
2 labels_npz_path="stardist/he.npz",
3 stardist_model="2D_versatile_he",
4 prob_thresh=0.1
5 )

File ~\miniconda3\envs\myenv\lib\site-packages\bin2cell\bin2cell.py:122, in stardist(image_path, labels_npz_path, stardist_model, block_size, min_overlap, context, **kwargs)
120 img = normalize(img)
121 #use pretrained stardist model
--> 122 model = StarDist2D.from_pretrained(stardist_model)
123 #will need to specify axes shortly, which are model dependent
124 if stardist_model == "2D_versatile_he":
125 #3D image, got the axes YXC from the H&E model config.json

File ~\miniconda3\envs\myenv\lib\site-packages\csbdeep\models\base_model.py:130, in BaseModel.from_pretrained(cls, name_or_alias)
128 try:
129 get_model_details(cls, name_or_alias, verbose=True)
--> 130 return get_model_instance(cls, name_or_alias)
131 except ValueError as e:
132 if name_or_alias is not None:

File ~\miniconda3\envs\myenv\lib\site-packages\csbdeep\models\pretrained.py:116, in get_model_instance(cls, key_or_alias)
115 def get_model_instance(cls, key_or_alias):
--> 116 path = get_model_folder(cls, key_or_alias)
117 model = cls(config=None, name=path.stem, basedir=path.parent)
118 model.basedir = None # make read-only

File ~\miniconda3\envs\myenv\lib\site-packages\csbdeep\models\pretrained.py:108, in get_model_folder(cls, key_or_alias)
106 path_folder = path_folder.with_name(path_folder.name[:-len(suffix)])
107 if not path_folder.exists():
--> 108 path_folder.symlink_to(path.relative_to(path.parent))
109 else:
110 path_folder = path.parent

File ~\miniconda3\envs\myenv\lib\pathlib.py:1403, in Path.symlink_to(self, target, target_is_directory)
1398 def symlink_to(self, target, target_is_directory=False):
1399 """
1400 Make this path a symlink pointing to the target path.
1401 Note the order of arguments (link, target) is the reverse of os.symlink.
1402 """
-> 1403 self._accessor.symlink(target, self, target_is_directory)

OSError: [WinError 1314] A required privilege is not held by the client: '2D_versatile_he_extracted' -> 'C:\Users\uCTImagingA\.keras\models\StarDist2D\2D_versatile_he\2D_versatile_he'

[ktpolanski]

Interesting, you seem unable to extract the model to its desired folder? Good thing there's a workaround function in #28

Download the 2D_versatile_he model from https://github.com/stardist/stardist-models/releases/tag/v0.1 and then load it like dfgao did, and then use the custom function I posted to use it.