diff --git a/doc/start_page.md b/doc/start_page.md index 3b26844..3e8d809 100644 --- a/doc/start_page.md +++ b/doc/start_page.md @@ -14,24 +14,53 @@ especially throught the [domain adaptation](domain-adaptation) functionality. SynapseNet offers a [napari plugin](napari-plugin), [command line interface](command-line-interface), and [python library](python-library). Please cite our [bioRxiv preprint](TODO) if you use it in your research. -**The rest of the documentation will be updated in the next days!** ## Requirements & Installation -- Requirements: Tested on Linux but should work on Mac/Windows. - - GPU needed to use 3d segmentation networks -- Installation via conda and local pip install - - GPU support +SynapseNet was developed and tested on Linux. It should be possible to install and use it on Mac or Windows, but we have not tested this. +Furthermore, SynapseNet requires a GPU for segmentation of 3D volumes. + +You need a [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) or [mamba](https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html) installation. Follow the instruction at the respective links if you have installed neither. We assume you have `conda` for the rest of the instructions. After installing it, you can use the `conda` command. + +To install it you should follow these steps: +- First, download the SynapseNet repository via +```bash +git clone https://github.com/computational-cell-analytics/synapse-net +``` +- Then, enter the `synapse-net` folder: +```bash +cd synapse-net +``` +- Now you can install the environment for SynapseNet with `conda` from the environment file we proved: +```bash +conda env create -f environment.yaml +``` +- You will need to confirm this step. It will take a while. Afterwards you can activate the environment: +```bash +conda activate synapse-net +``` +- Finally, install SynapseNet itself into the environment: +```bash +pip install -e . +``` + +Now you can use all SynapseNet features. From now on, just activate the environment via +``` +conda activate synapse-net +``` +to use them. + +> Note: If you use `mamba` instead of conda just replace `conda` in the commands above with `mamba`. + +> Note: We also provide an environment for a CPU version of SynapseNet. You can install it by replacing `environment.yaml` with `environment_cpu.yaml` in the respective command above. This version can be used for 2D vesicle segmentation, but it does not work for 3D segmentation. + +> Note: If you have issues with the CUDA version then install a PyTorch that matches your nvidia drivers. See [pytorch.org](https://pytorch.org/) for details. -- Make sure conda or mamba is installed. - - If you don't have a conda installation yet we recommend [micromamba](https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html) -- Create the environment with all required dependencies: `mamba env create -f environment.yaml` -- Activate the environment: `mamba activate synaptic-reconstruction` -- Install the package: `pip install -e .` ## Napari Plugin -lorem ipsum +**The rest of the documentation will be updated in the next days!** + ## Command Line Functionality @@ -40,6 +69,7 @@ lorem ipsum - vesicles / spheres - objects + ## Python Library - segmentation functions diff --git a/environment.yaml b/environment.yaml index 82644b0..b669bbd 100644 --- a/environment.yaml +++ b/environment.yaml @@ -1,17 +1,22 @@ channels: + - pytorch + - nvidia - conda-forge name: - synaptic-reconstruction + synapse-net dependencies: - - python-elf + - bioimageio.core + - kornia + - magicgui - napari - pip - pyqt - - magicgui + - python-elf - pytorch - - bioimageio.core - - kornia + - pytorch-cuda=12.4 - tensorboard + - torch_em + - torchvision - trimesh - pip: - napari-skimage-regionprops diff --git a/environment_cpu.yaml b/environment_cpu.yaml new file mode 100644 index 0000000..5c68976 --- /dev/null +++ b/environment_cpu.yaml @@ -0,0 +1,18 @@ +channels: + - conda-forge +name: + synapse-net +dependencies: + - bioimageio.core + - kornia + - magicgui + - napari + - pip + - pyqt + - python-elf + - pytorch + - tensorboard + - torch_em + - trimesh + - pip: + - napari-skimage-regionprops diff --git a/plot_distances.sh b/plot_distances.sh deleted file mode 100755 index 5e4b1b1..0000000 --- a/plot_distances.sh +++ /dev/null @@ -1 +0,0 @@ -sr_tools.measure_distances -i /home/pape/Work/data/moser/lipids-julia/corrected_tomos_mrc/TS01.mrc_10.00Apx_corrected.mrc -s /home/pape/Work/data/moser/lipids-julia/results/v1/labels-center-membrane/TS01.mrc_10.00Apx_corrected.tif -m /home/pape/Work/data/moser/lipids-julia/results/v1/distance_measurements/TS01.mrc_10.00Apx_corrected.npz