pyDoric

This repository contains python scripts and Pyinstaller spec files that are used to create executable files. These executables are distributes as libraries of danse software.

MiniAn

---

To create MiniAn executable, follow the steps:

1. Create new environment, and install MiniAn and PyInstaller by running the following in Anaconda prompt:

   conda create -n minian_pyinstaller -c bioconda -c conda-forge python=3.8 minian=1.2.1 h5py pyinstaller pefile=2023.2.7 --yes
   

   conda activate minian_pyinstaller
   

   ⚠️ It may take some time to install.

   For more information about the library, please read MiniAn docs.

2. Clone this repository. In Anaconda prompt, navigate to the directory where the repository was cloned.

3. Package the code into an executable by using pyinstaller spec file and running the following in Anaconda prompt:

   cd Deploy
   

   pyinstaller pack_minian_run.spec
   

CaImAn

---

To create CaImAn executable, follow the steps:

1. Create new environment, and install CaImAn and PyInstaller by running the following in Anaconda prompt:

   conda create -n caiman_pyinstaller -c conda-forge python=3.10.8 caiman=1.11.4 pyinstaller pefile=2023.2.7 ipyparallel=8.8.0 --yes
   

   conda activate caiman_pyinstaller
   

   ⚠️ It may take some time to install.

   For more information about the library, please read CaImAn docs.

2. Clone this repository. In Anaconda prompt, navigate to the directory where the repository was cloned.

3. Use CaImAn manager to finish the istallation by running in Anaconda prompt:

   caimanmanager install
   

   This would add 'caiman_data' folder into your user folder 'C:\Users\your_user_name'. Copy this this folder into your cloned 'CaImAn' folder.

4. Package the code into an executable by using pyinstaller spec file and running the following in Anaconda prompt:

   cd Deploy
   

   pyinstaller pack_caiman_run.spec
   

Suite2p

---

To create Suite2p executable, follow the steps:

1. Create new environment, and install CaImAn and PyInstaller by running the following lines in Anaconda prompt:

   conda create --name suite2p_pyinstaller python=3.9 pyinstaller h5py --yes
   

   conda activate suite2p_pyinstaller
   

   python -m pip install suite2p
   

   For more information about the library, please read Suite2p docs.

2. Clone this repository. In Anaconda prompt, navigate to the directory where the repository was cloned.

3. Package the code into an executable by using pyinstaller spec file and running the following in Anaconda prompt:

   cd Deploy
   

   pyinstaller pack_suite2p_run.spec
   

DeepLabCut

---

1. Install CUDA v12.6

2. Install cuDNN v9.6

3. Create new environment, and install DeepLabCut and PyInstaller by running the following in Anaconda prompt:

   conda create -n deeplabcut_pyinstaller -c conda-forge python=3.10 pytables==3.8.0 pyinstaller h5py --yes
   

   conda activate deeplabcut_pyinstaller
   

   pip install --upgrade --index-url https://download.pytorch.org/whl/cu128 torch==2.8.0+cu128 torchvision==0.23.0+cu128
   

   Note: set your CUDA version in the prompt above

   pip install "deeplabcut==3.0.0rc8"
   

   For more information about the library, please read DeepLabCut docs.

4. Clone this repository. In Anaconda prompt, navigate to the directory where the repository was cloned.

5. Package the code into an executable by using pyinstaller spec file and running the following in Anaconda prompt:

   cd Deploy
   

   pyinstaller pack_deeplabcut_run.spec