diff --git a/docs/chapters/getting_started/installation.md b/docs/chapters/getting_started/installation.md index 51f6a996..222968d3 100644 --- a/docs/chapters/getting_started/installation.md +++ b/docs/chapters/getting_started/installation.md @@ -56,7 +56,6 @@ PlantSeg can be installed directly by executing in the terminal (or PowerShell o mamba create -n plant-seg -c pytorch -c nvidia -c conda-forge pytorch cpuonly plant-seg --no-channel-priority ``` - === "Windows" * NVIDIA GPU version, CUDA=12.x @@ -82,7 +81,7 @@ PlantSeg can be installed directly by executing in the terminal (or PowerShell o * Apple silicon version ```bash - mamba create -n plant-seg -c pytorch -c conda-forge python=3.11 pytorch::pytorch pyqt plant-seg --no-channel-priority + mamba create -n plant-seg -c pytorch -c conda-forge python=3.11 pytorch::pytorch plant-seg --no-channel-priority ``` If you used older versions of PlantSeg, please delete the old config files in `~/.plantseg_models/configs/` after installing new PlantSeg. @@ -93,24 +92,14 @@ Please refer to the [PyTorch](https://pytorch.org/get-started/locally/) website ## Optional dependencies -If you want to use the headless mode of PlantSeg, you need to install `dask[distributed]`: - -```bash -conda activate plant-seg -mamba install dask distributed -``` - -Some types of compressed tiff files require an additional package to be load correctly (e.g.: Zlib, ZSTD, LZMA, ...). -To run PlantSeg on those stacks, you need to install `imagecodecs`. -In the terminal: +Certain compressed TIFF files (e.g., Zlib, ZSTD, LZMA formats) require additional codecs to be processed correctly by PlantSeg. To handle such files, install the `imagecodecs` package: ```bash conda activate plant-seg pip install imagecodecs ``` -Experimental support for SimpleITK watershed segmentation has been added to PlantSeg version 1.1.8. -These features can be used only after installing the SimpleITK package: +If you plan to use SimpleITK-based watershed segmentation, you will need to install `SimpleITK` as an additional dependency: ```bash conda activate plant-seg diff --git a/environment-elife.yml b/environment-elife.yml index 637505a6..2432b819 100644 --- a/environment-elife.yml +++ b/environment-elife.yml @@ -1,4 +1,4 @@ -name: plant_seg +name: plant-seg-elife channels: - pytorch - cpape @@ -136,4 +136,3 @@ dependencies: - werkzeug==0.16.0 - wrapt==1.11.2 prefix: /home/lcerrone_local/miniconda3/envs/plant_seg - diff --git a/environment.yaml b/environment.yaml index 73104897..13f1c2e2 100644 --- a/environment.yaml +++ b/environment.yaml @@ -17,6 +17,7 @@ dependencies: - scikit-image - bioimageio.core>=0.6.5 # GUI + - pyqt - napari # Other - requests