Update README

Author: constantinpape

README.md

@@ -8,11 +8,15 @@ We implement napari applications for:
 
 **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.
+This is an early beta version. Any feedback is welcome, but please be aware that the functionality is under active development and that several features are not finalized or thoroughly tested yet.
+Once the functionality has matured we plan to release the interactive annotation applications as [napari plugins](https://napari.org/stable/plugins/index.html).
+
 
 ## Functionality overview
 
 TODO
+- quick explanation and gifs
+
 
 ## Installation
 
@@ -51,15 +55,32 @@ pip install -e .
 
 ## Usage
 
+After the installation the three applications for interactive annotations can be started from the command line or within a python script:
+- **2d annotation**: via the command `micro_sam.annotator_2d` or with the function `micro_sam.sam_annotator.annotator_2d` from python. Run `micro_sam.annotator_2d -h` or check out [examples/sam_annotator_2d](https://github.com/computational-cell-analytics/micro-sam/blob/master/examples/sam_annotator_2d.py) for details. 
+- **3d annotation**: via the command `micro_sam.annotator_3d` or with the function `micro_sam.sam_annotator.annotator_3d` from python. Run `micro_sam.annotator_3d -h` or check out [examples/sam_annotator_3d](https://github.com/computational-cell-analytics/micro-sam/blob/master/examples/sam_annotator_3d.py) for details. 
+- **tracking**: via the command `micro_sam.annotator_tracking` or with the function `micro_sam.sam_annotator.annotator_tracking` from python. Run `micro_sam.annotator_tracking -h` or check out [examples/sam_annotator_tracking](https://github.com/computational-cell-analytics/micro-sam/blob/master/examples/sam_annotator_tracking.py) for details. 
+
 TODO
+- show image with annotated user interface (for 3d?!)
+- link to videos that explain the functionality for the 3 plugins
 
 ### Tips & Tricks
 
 TODO
+- speeding things up: precomputing the embeddings with a gpu, making input images smaller
+- correcting existing segmentaitons via `segmentation_results`
+- saving and loading intermediate results via segmentation results
+
+### Limitations
+
+TODO
+- automatic instance segmentation limitations
 
 ## Using the micro_sam library
 
 TODO
+- link to the example image series application
+
 
 ## Contributing
 
@@ -68,6 +89,7 @@ micro_sam <- library with utility functionality for using SAM for microscopy dat
     /sam_annotator <- the napari plugins for annotation
 ```
 
+
 ## Citation
 
 If you are using this repository in your research please cite