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Update app.py
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app.py
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@@ -9,17 +9,26 @@ from PIL import Image
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import io
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from huggingface_hub import hf_hub_download
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@spaces.GPU
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def segment_and_count(image):
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# Initialize model inside the GPU-decorated function
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model = models.CellposeModel(gpu=True, pretrained_model=model_path)
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# Convert PIL Image to numpy array
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image_np = np.array(image)
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@@ -64,13 +73,16 @@ def segment_and_count(image):
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# Gradio interface
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demo = gr.Interface(
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fn=segment_and_count,
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inputs=
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outputs=[
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gr.Number(label="Number of Cells"),
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gr.Image(type="pil", label="Segmented Overlay")
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],
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title="Cell Counter with Cellpose",
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description="Upload a microscopy image and count the number of cells using Cellpose segmentation."
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)
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if __name__ == "__main__":
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import io
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from huggingface_hub import hf_hub_download
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HF_REPO_ID = "myang4218/cellposemodel"
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MODEL_OPTIONS = {
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"Hemocytometer Model": "hemocytometermodel.npy",
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"General Model": "generalmodel.npy"
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}
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loaded_models = {}
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@spaces.GPU
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def segment_and_count(image, model_choice):
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model_filename = MODEL_OPTIONS[model_choice]
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model_path = hf_hub_download(repo_id=HF_REPO_ID, filename=model_filename)
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if model_filename in loaded_models:
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model = loaded_models[model_filename]
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else:
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model = models.CellposeModel(gpu=True, pretrained_model=model_path)
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loaded_models[model_filename] = model
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# Convert PIL Image to numpy array
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image_np = np.array(image)
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# Gradio interface
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demo = gr.Interface(
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fn=segment_and_count,
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inputs=[
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gr.Image(type="pil", label="Microscopy Image"),
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gr.Dropdown(choices=list(MODEL_OPTIONS.keys()), label="Select Model", value="Hemocytometer Model")
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],
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outputs=[
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gr.Number(label="Number of Cells"),
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gr.Image(type="pil", label="Segmented Overlay")
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],
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title="Cell Counter with Cellpose",
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description="Upload a microscopy image and select a model to count the number of cells using Cellpose segmentation."
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)
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if __name__ == "__main__":
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