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Dockerfile

@@ -1,5 +1,11 @@
 FROM python:3.12-slim-bullseye
+COPY --from=ghcr.io/astral-sh/uv:0.5.30 /uv /bin/uv
 
+ENV PYTHONUNBUFFERED=1
+ENV PYTHONIOENCODING=UTF-8
+ENV UV_COMPILE_BYTECODE=1
+ENV UV_NO_CACHE=1
+ENV PATH="/app/.venv/bin:$PATH"
 
 RUN apt-get update && apt-get install -y \
     build-essential \
@@ -8,16 +14,20 @@ RUN apt-get update && apt-get install -y \
     git \
     && rm -rf /var/lib/apt/lists/*
 
+RUN useradd -m -u 1000 user
+USER user
 WORKDIR /app
-COPY requirements.txt /app/requirements.txt
+RUN chown -R user:user /app
+RUN chown -R user:user /home/user
+
+COPY README.md /app/
+COPY pyproject.toml /app/
 COPY pages /app/pages
 COPY run.py /app/run.py
-
-RUN pip3 install --upgrade pip
-RUN pip3 install -r requirements.txt
+RUN uv sync
 
 EXPOSE 8501
 
 HEALTHCHECK CMD curl --fail http://localhost:8501/_stcore/health
 
-ENTRYPOINT ["streamlit", "run", "run.py", "--server.port=8501", "--server.address=0.0.0.0"]
+ENTRYPOINT ["uv", "run", "streamlit", "run", "run.py", "--server.port=8501", "--server.address=0.0.0.0"]

pages/SDH_staining.py

@@ -33,8 +33,8 @@ use_GPU = is_gpu_availiable()
 
 
 @st.cache_resource
-def st_load_sdh_model(model_path):
-    return load_sdh_model(model_path)
+def st_load_sdh_model():
+    return load_sdh_model()
 
 
 @st.cache_resource
@@ -78,19 +78,13 @@ tf.random.set_seed(42)
 np.random.seed(42)
 
 
-if path.exists("model.h5"):
-    st.success("SDH Model ready to use !")
-    pass
-else:
-    with st.spinner("Please wait we are downloading the SDH Model."):
-        urllib.request.urlretrieve(
-            "https://lbgi.fr/~meyer/SDH_models/model.h5", "model.h5"
-        )
-    st.success("SDH Model have been downloaded !")
 
-model_cellpose = st_load_cellpose()
+with st.spinner("Please wait we are loading the SDH Model."):
+    model_SDH = st_load_sdh_model()
 
-model_SDH = st_load_sdh_model("model.h5")
+st.success("SDH Model have been downloaded !")
+
+model_cellpose = st_load_cellpose()
 
 st.title("SDH Staining Analysis")
 st.write(

pyproject.toml

@@ -0,0 +1,15 @@
+[project]
+name = "myoquant-streamlit"
+version = "0.1.0"
+description = ""
+readme = "README.md"
+requires-python = "<3.13, >=3.12"
+dependencies = [
+    "myoquant>=0.3.8",
+    "streamlit",
+    "pandas",
+    "numpy",
+    "imageio",
+    "matplotlib",
+    "requests",
+]

run.py

@@ -11,36 +11,31 @@ navigation_dict = {
         st.Page(
             page="pages/home.py",
             title="Home",
-            icon="👨‍👨‍👦‍👦",
-            url_path="home",
+            icon="🏠",
             default=True,
         ),
         st.Page(
             page="pages/ATP_staining.py",
             title="ATP Staining",
-            icon="👨‍👨‍👦‍👦",
-            url_path="atp_staining",
+            icon="🟣",
             default=False,
         ),
         st.Page(
             page="pages/HE_staining.py",
             title="HE Staining",
-            icon="👨‍👨‍👦‍👦",
-            url_path="he_staining",
+            icon="🔴",
             default=False,
         ),
         st.Page(
             page="pages/SDH_staining.py",
             title="SDH Staining",
-            icon="👨‍👨‍👦‍👦",
-            url_path="sdh_staining",
+            icon="🔵",
             default=False,
         ),
         st.Page(
             page="pages/Fluo_staining.py",
             title="Fluo Staining",
-            icon="👨‍👨‍👦‍👦",
-            url_path="fluo_staining",
+            icon="🟢",
             default=False,
         ),
     ],