diff --git a/doc/annotation_tools.md b/doc/annotation_tools.md index 71491b7d..4692ed1a 100644 --- a/doc/annotation_tools.md +++ b/doc/annotation_tools.md @@ -19,11 +19,18 @@ The annotation tools can be started from the napari plugin menu: You can find additional information on the annotation tools [in the FAQ section](#usage-question). +HINT: If you would like to start napari to use `micro-sam` from the plugin menu, you must start it by activating the environment where `micro-sam` has been installed using: + +```bash +$ mamba activate +$ napari +``` + ## Annotator 2D The 2d annotator can be started by -- clicking `Annotator 2d` in the plugin menu. +- clicking `Annotator 2d` in the plugin menu after starting `napari`. - running `$ micro_sam.annotator_2d` in the command line. - calling `micro_sam.sam_annotator.annotator_2d` in a python script. Check out [examples/annotator_2d.py](https://github.com/computational-cell-analytics/micro-sam/blob/master/examples/annotator_2d.py) for details. @@ -55,7 +62,7 @@ Check out [the video tutorial](https://youtu.be/9xjJBg_Bfuc) for an in-depth exp ## Annotator 3D The 3d annotator can be started by -- clicking `Annotator 3d` in the plugin menu. +- clicking `Annotator 3d` in the plugin menu after starting `napari`. - running `$ micro_sam.annotator_3d` in the command line. - calling `micro_sam.sam_annotator.annotator_3d` in a python script. Check out [examples/annotator_3d.py](https://github.com/computational-cell-analytics/micro-sam/blob/master/examples/annotator_3d.py) for details. @@ -81,7 +88,7 @@ Check out [the video tutorial](https://youtu.be/nqpyNQSyu74) for an in-depth exp ## Annotator Tracking The tracking annotator can be started by -- clicking `Annotator Tracking` in the plugin menu. +- clicking `Annotator Tracking` in the plugin menu after starting `napari`. - running `$ micro_sam.annotator_tracking` in the command line. - calling `micro_sam.sam_annotator.annotator_tracking` in a python script. Check out [examples/annotator_tracking.py](https://github.com/computational-cell-analytics/micro-sam/blob/master/examples/annotator_tracking.py) for details. @@ -107,7 +114,7 @@ Check out [the video tutorial](https://youtu.be/1gg8OPHqOyc) for an in-depth exp ## Image Series Annotator The image series annotation tool enables running the [2d annotator](#annotator-2d) or [3d annotator](#annotator-3d) for multiple images that are saved in a folder. This makes it convenient to annotate many images without having to restart the tool for every image. It can be started by -- clicking `Image Series Annotator` in the plugin menu. +- clicking `Image Series Annotator` in the plugin menu after starting `napari`. - running `$ micro_sam.image_series_annotator` in the command line. - calling `micro_sam.sam_annotator.image_series_annotator` in a python script. Check out [examples/image_series_annotator.py](https://github.com/computational-cell-analytics/micro-sam/blob/master/examples/image_series_annotator.py) for details. @@ -126,7 +133,7 @@ Check out [the video tutorial](https://youtu.be/HqRoImdTX3c) for an in-depth exp ## Finetuning UI -We also provide a graphical inferface for fine-tuning models on your own data. It can be started by clicking `Finetuning` in the plugin menu. +We also provide a graphical inferface for fine-tuning models on your own data. It can be started by clicking `Finetuning` in the plugin menu after starting `napari`. **Note:** if you know a bit of python programming we recommend to use a script for model finetuning instead. This will give you more options to configure the training. See [these instructions](#training-your-own-model) for details. diff --git a/doc/installation.md b/doc/installation.md index 5fb23278..969cb2ef 100644 --- a/doc/installation.md +++ b/doc/installation.md @@ -22,13 +22,23 @@ You can follow the instructions [here](https://mamba.readthedocs.io/en/latest/in $ mamba install -c pytorch -c conda-forge micro_sam ``` or you can create a new environment (here called `micro-sam`) via: + ```bash $ mamba create -c pytorch -c conda-forge -n micro-sam micro_sam ``` + if you want to use the GPU you need to install PyTorch from the `pytorch` channel instead of `conda-forge`. For example: + ```bash $ mamba create -c pytorch -c nvidia -c conda-forge -n micro-sam micro_sam pytorch pytorch-cuda=12.1 ``` + +NOTE: If you create a new enviroment (eg. here called `micro-sam`), you must activate the environment using + +```bash +$ mamba activate micro-sam +``` + You may need to change this command to install the correct CUDA version for your system, see [https://pytorch.org/](https://pytorch.org/) for details. diff --git a/doc/start_page.md b/doc/start_page.md index 74032485..9364b20b 100644 --- a/doc/start_page.md +++ b/doc/start_page.md @@ -22,12 +22,17 @@ If you run into any problems or have questions please [open an issue](https://gi ## Quickstart You can install `micro_sam` via mamba: -``` +```bash $ mamba install -c conda-forge micro_sam ``` We also provide installers for Windows and Linux. For more details on the available installation options, check out [the installation section](#installation). -After installing `micro_sam` you can start napari and select the annotation tool you want to use from `Plugins -> SegmentAnything for Microscopy`. Check out the [quickstart tutorial video](https://youtu.be/gcv0fa84mCc) for a short introduction and [the annotation tool section](#annotation-tools) for details. +After installing `micro_sam`, you can start napari from within your environment using + +```bash +$ napari +``` +After starting napari, you can select the annotation tool you want to use from `Plugins -> SegmentAnything for Microscopy`. Check out the [quickstart tutorial video](https://youtu.be/gcv0fa84mCc) for a short introduction and [the annotation tool section](#annotation-tools) for details. The `micro_sam` python library can be imported via