python_for_microscopists

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I tried to feed my model trained as suggested, but when I feed the model to SamAutomaticMaskGenerator or SamPredictor it doesn't work. How can I make it generate masks for...

Barryjuait

OSError: No file or directory found at models/satellite_standard_unet_100epochs.hdf5

2

Hello All. when i executed semantic segmentation using unet code for 100 epochs, i got memory exhausted error and now i upgraded my system to 16GB RAM and i7 processor...

nagamani-g

expanding dimension to solve the dimension incompatibility

1

Solving value error in code block 55: --------------------------------------------------------------------------- ValueError Traceback (most recent call last) in () 23 #inputs = processor(single_patch, return_tensors="pt") 24 #Now try with bounding boxes. Remember to uncomment....

sanjeev4427

Without expanding dimension the following error comes up in while executing code block 33: example = train_dataset[0] for k,v in example.items(): print(k,v.shape) --------------------------------------------------------------------------- ValueError Traceback (most recent call last) in...

sanjeev4427

file "/usr/lib/python3.8/codecs.py", line 322, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) UnicodeDecodeError: 'utf-8' codec can't decode byte 0x80 in position 64: invalid start byte This error occurs for the...

bhandaripratibha06

I have followed the 293_denoising_RGB_images_using_deep_learning.ipynb and everything seemed fine except while trying to predict. This is the error that I get: `pred = model.predict(img, axes='YXC') --------------------------------------------------------------------------- ValueError Traceback (most recent...

astronerdF

Overlapping instances in fine-tuning SAM

2

Hello @bnsreenu Thanks for providing the repo for fine-tuning the SAM model on the custom dataset. My question is that in case where the instances of the object are overlapping...

Ashutosh1995

In 331_fine_tune_SAM_mito.ipynb, the class SAMDataset(Dataset) needs to be adjusted to have 3 bands to go into the processor

5

The demo no longer works. Change this line in the class SAMDataset(Dataset) ` # prepare image and prompt for the model inputs = self.processor(image, input_boxes=[[prompt]], return_tensors="pt")` to ` # prepare...

throughthetrees

Hi @bnsreenu, This is my first time analysing bioimages and I am trying out different models but started with STARdist. This is IF image and I want to perform nuclei...

apal6

When I try to train om my own images and segmentation maps I get this: .../mmsegmentation/mmseg/datasets/transforms/formatting.py:81: UserWarning: Please pay attention your ground truth segmentation map, usually the segmentation map is...

jhaggle