Adding a Dockerfile for application, requirements and improvements fo…

Dockerfile

@@ -0,0 +1,61 @@
+# Dockerfile by Sebastián Sterling
+FROM accetto/ubuntu-vnc-xfce-g3:latest
+
+USER root
+
+WORKDIR /Cellpose
+
+
+# Install Packages
+RUN apt-get clean && rm -rf /var/lib/apt/lists/* && \
+    apt-get update --fix-missing && \
+    apt-get upgrade -y && \
+    apt-get install -y --no-install-recommends \
+    ffmpeg \
+    vim \
+    git \
+    python3-pip \
+    mesa-common-dev \
+    libgl1-mesa-dri \
+    libxcb-cursor0 \
+    mesa-utils \
+    libsm6 \
+    libxext6 \
+    libxrender1 \
+    libfontconfig1 \
+    libxkbcommon-x11-0 \
+    libxcb-xinerama0 \
+    libxcb-icccm4 \
+    libxcb-image0 \
+    libxcb-keysyms1 \
+    libxcb-render-util0 \
+    libxcb-xfixes0 \
+    libturbojpeg \
+    libjpeg-dev \
+    zlib1g-dev \
+    build-essential \ 
+    && rm -rf /var/lib/apt/lists/*
+
+RUN apt update && apt upgrade -y
+COPY requirements.txt .
+
+
+#### Install Cellpose ####
+RUN pip3 install --break-system-packages torch torchvision --index-url https://download.pytorch.org/whl/cu126 
+RUN pip3 install --break-system-packages git+https://www.github.com/mouseland/cellpose.git 
+RUN pip3 install --break-system-packages 'cellpose[gui]' 
+RUN pip3 install --break-system-packages cellpose
+#### Install Cellpose ####
+
+
+ENV VNC_PW=@Pass-Word4321 \
+    VNC_RESOLUTION=1280x800
+
+CMD ["python3", "-m", "cellpose"]
+
+# sudo docker build -t cellpose-web .
+# sudo docker run -d --name cellpose-vnc -p 36901:6901 --hostname quick cellpose-web
+
+# To run it with GPUS
+# sudo docker run -d --name cellpose-vnc --gpus all -p 36901:6901 --hostname quick cellpose-web
+

README.md

@@ -125,13 +125,90 @@ Venv ([tutorial](https://docs.python-guide.org/dev/virtualenvs/#lower-level-virt
 
 If you are using a GPU, make sure its drivers and the cuda libraries are correctly installed.
 
-1. Install python3.8 or later from [python.org](https://www.python.org/downloads/). This will be the version of python that will be used in the environment. You can check your python version with `python --version`.
-2. Navigate to the directory where you want to create the environment and run `python3 -m venv cellpose` to create a new environment called `cellpose`.
-3. Activate the environment with `source cellpose/bin/activate` on Mac/Linux or `cellpose\Scripts\activate` on Windows. A prefix `(cellpose)` should appear in the terminal.
-4. Install cellpose into the `cellpose` venv using pip with `python -m pip install cellpose`.
-5. Install the cellpose GUI, with `python -m pip install cellpose[gui]`. Depending on your terminal software, you may need to use quotes like this: `python -m pip install 'cellpose[gui]'`.
-6. You can now run cellpose from this environment with `python -m cellpose` or `cellpose` if you are in the cellpose directory.
-7. To deactivate the environment, run `deactivate`. 
+#### 1. Install python3.8 or later from [python.org](https://www.python.org/downloads/). This will be the version of python that will be used in the environment. You can check your python version with:
+```bash
+python --version
+```
+#### 2. Navigate to the directory where you want to create the environment and run:  
+```bash
+python3 -m venv cellpose
+```
+#### to create a new environment called `cellpose`.
+#### 3. Activate the environment with:
+```bash
+source cellpose/bin/activate 
+```
+#### on Mac/Linux or:
+```bash
+cellpose\Scripts\activate
+```
+#### on Windows. A prefix `(cellpose)` should appear in the terminal.
+
+#### 4. Install cellpose into the `cellpose` venv using pip with:
+```bash
+python -m pip install cellpose
+```
+
+#### 5. Install the cellpose GUI, with:
+```bash
+python -m pip install cellpose[gui]
+```
+#### Depending on your terminal software, you may need to use quotes like this:
+```bash
+python -m pip install 'cellpose[gui]'
+```
+
+#### 6. You can now run cellpose from this environment with:
+```bash
+python -m cellpose`
+```
+#### or
+```bash
+cellpose
+```
+#### if you are in the cellpose directory, and you can also run cellpose on the Background adding `&` at the end of the command.
+
+#### 7. If there's any missed package, you can try using:
+```bash
+pip install -r requirements.txt
+```
+
+#### 8. To deactivate the environment, run:
+```bash
+deactivate
+``` 
+
+### Option 3: Installation instruction using Docker
+Docker is an open-source platform to automates the deployment of applications within lightweight, portable containers. This is crucial for modern application development, as it simplifies the deployment process it also improves resources efficiency.
+
+To run the following commands, make sure you have previously installed [Docker](https://docs.docker.com/engine/install/).
+
+#### 1. You can create and edit the image with the `Dockerfile` in the repository.
+#### To create, you use (in the same directory of Dockerfile):
+```bash
+sudo docker build cellpose-vnc-image .
+```
+#### Or you can Pull the image from [DockerHub](https://hub.docker.com/r/sethsterling/ubuntu-vnc-xfce-cellpose-gui):
+```bash
+sudo docker pull sethsterling/ubuntu-vnc-xfce-cellpose-gui:latest
+```
+
+
+#### 2. Run the container using:
+
+```bash
+sudo docker run -d --name cellpose-vnc -p 36901:6901 --hostname quick sethsterling/ubuntu-vnc-xfce-cellpose-gui:latest
+
+# To run it with GPUS
+sudo docker run -d --name cellpose-vnc --gpus all -p 36901:6901 --hostname quick sethsterling/ubuntu-vnc-xfce-cellpose-gui:latest
+```
+
+#### 3. Enter to your device ip with port `36901` (as placed in the `docker run` command) (e.g. [127.0.0.0:36901](http://127.0.0.0:36901)).
+
+#### 4. Put the password: `@Pass-Word4321` as default, or you can change it adding: `-e VNC_PW=[Your_Custom_Password]` in the `docker run` command.
+
+#### 5. You must be interested on setting the file transfer between your system and the container, in that case you should set up a volume using the flag `-v /path/to/your/files/:/Cellpose` in the `docker run` command.
+
 
 ### GPU version (CUDA) on Windows or Linux
 

requirements.txt

@@ -0,0 +1,49 @@
+cellpose @ git+https://www.github.com/mouseland/cellpose.git@9e5cc9cc70fdafe3442e21189d2d4eaf2c87425a
+fastremap==1.17.1
+filelock==3.13.1
+fill_voids==2.1.0
+fsspec==2024.6.1
+imagecodecs==2025.3.30
+Jinja2==3.1.4
+MarkupSafe==2.1.5
+mpmath==1.3.0
+natsort==8.4.0
+networkx==3.3
+numpy==1.26.4
+nvidia-cublas-cu12==12.6.4.1
+nvidia-cuda-cupti-cu12==12.6.80
+nvidia-cuda-nvrtc-cu12==12.6.77
+nvidia-cuda-runtime-cu12==12.6.77
+nvidia-cudnn-cu12==9.5.1.17
+nvidia-cufft-cu12==11.3.0.4
+nvidia-cufile-cu12==1.11.1.6
+nvidia-curand-cu12==10.3.7.77
+nvidia-cusolver-cu12==11.7.1.2
+nvidia-cusparse-cu12==12.5.4.2
+nvidia-cusparselt-cu12==0.6.3
+nvidia-nccl-cu12==2.26.2
+nvidia-nvjitlink-cu12==12.6.85
+nvidia-nvtx-cu12==12.6.77
+opencv-python-headless==4.11.0.86
+packaging==25.0
+pillow==11.0.0
+Pygments==2.19.2
+PyQt6==6.9.1
+PyQt6-Qt6==6.9.1
+PyQt6_sip==13.10.2
+pyqtgraph==0.13.7
+QtPy==2.4.3
+roifile==2025.5.10
+scipy==1.16.0
+segment-anything==1.0
+setuptools==68.1.2
+superqt==0.7.5
+sympy==1.13.3
+tifffile==2025.6.11
+torch==2.7.1+cu126
+torchvision==0.22.1+cu126
+tqdm==4.67.1
+triton==3.3.1
+typing_extensions==4.12.2
+urllib3==2.0.7
+wheel==0.42.0