Add README and environment files

Author: constantinpape

README.md

@@ -1,16 +1,60 @@
 # SegmentAnything for Microscopy
 
-## Installation and Requirements
+Tools for segmentation and tracking in microscopy build on top of [SegmentAnything](https://segment-anything.com/).
+We implement napari applications for:
+- interactive 2d segmentation
+- interactive 3d segmentation
+- interactive tracking of 2d image data
 
-Install [PyTorch](https://pytorch.org/get-started/locally/), [SegmentAnything](https://github.com/facebookresearch/segment-anything#installation) and elf in your conda env.
-Then install the `micro_sam` library via
+**Early beta version**
+This is an early beta version. Any feedback is welcome, but please be aware that the functionality is evolving fast and not fully tested.
+
+## Functionality overview
+
+TODO
+
+## Installation
+
+You need to install [PyTorch](https://pytorch.org/get-started/locally/), [SegmentAnything](https://github.com/facebookresearch/segment-anything#installation), [napari](https://napari.org/stable/) and [elf](https://github.com/constantinpape/elf).
+We recommend to use conda and provide two conda environment files with all necessary requirements:
+- `environment_gpu.yaml`: sets up an environment with GPU support.
+- `environment_cpu.yaml`: sets up an environment with CPU support.
+
+You can create the corresponding environment via 
+
+```
+conda env create -f <ENV_FILE>.yaml
+```
+You can then activate the environment via
+```
+conda activate sam
+```
+And install our napari applications and the `micro_sam` library via
 ```
 pip install -e .
 ```
 
-## Structure
+## Usage
+
+TODO
+
+### Tips & Tricks
+
+TODO
+
+## Using the micro_sam library
+
+TODO
+
+## Contributing
 
 ```
 micro_sam <- library with utility functionality for using SAM for microscopy data
     /sam_annotator <- the napari plugins for annotation
 ```
+
+## Citation
+
+If you are using this repository in your research please cite
+- [SegmentAnything](https://arxiv.org/abs/2304.02643)
+- and our repository on [zenodo](TODO) (we are working on a full publication)

environment_cpu.yaml

@@ -0,0 +1,14 @@
+channels:
+    - pytorch
+    - conda-forge
+name:
+    sam
+dependencies:
+    - cpuonly
+    - napari
+    - python-elf
+    - pytorch
+    - torchvision
+    - tqdm
+    - pip:
+        - git+https://github.com/facebookresearch/segment-anything.git

environment_gpu.yaml

@@ -0,0 +1,15 @@
+channels:
+    - pytorch
+    - nvidia
+    - conda-forge
+name:
+    sam
+dependencies:
+    - napari
+    - python-elf
+    - pytorch
+    - pytorch-cuda>=11.7  # you may need to update the cuda version to match your system
+    - torchvision
+    - tqdm
+    - pip:
+        - git+https://github.com/facebookresearch/segment-anything.git