Update installer instructions

Author: constantinpape

doc/installation.md

@@ -1,6 +1,11 @@
 # Installation
 
-`micro_sam` requires the following dependencies:
+We provide three different ways of installing `micro_sam`:
+- [From conda](#from-conda) is the recommended way if you want to use all functionality.
+- [From source](#from-source) for setting up a development environment to change and potentially contribute to our software.
+- [From installer](#from-installer) to install without having to use conda. This mode of installation is still experimental! It only provides the annotation tools and does not enable model finetuning.
+
+Our software requires the following dependencies:
 - [PyTorch](https://pytorch.org/get-started/locally/)
 - [SegmentAnything](https://github.com/facebookresearch/segment-anything#installation)
 - [elf](https://github.com/constantinpape/elf)
@@ -14,7 +19,7 @@
 $ conda install -c conda-forge micro_sam
 ```
 
-This command will only install the `micro_sam` library without the required dependencies for the annotation functionality and training.
+This command will not install the required dependencies for the annotation tools and for training / finetuning.
 To use the annotation functionality you also need to install `napari`:
 ```
 $ conda install -c conda-forge napari pyqt
@@ -27,40 +32,6 @@ $ conda install -c conda-forge torch_em
 In case the installation via conda takes too long consider using [mamba](https://mamba.readthedocs.io/en/latest/).
 Once you have it installed you can simply replace the `conda` commands with `mamba`.
 
-## From installer
-
-We also provide installers for Linux, Mac and Windows:
-- [Linux](https://owncloud.gwdg.de/index.php/s/Cw9RmA3BlyqKJeU)
-- [Mac](https://owncloud.gwdg.de/index.php/s/7YupGgACw9SHy2P)
-- [Windows](https://owncloud.gwdg.de/index.php/s/1iD1eIcMZvEyE6d)
-
-Note that these installers are stil experimental and not yet fully tested.
-If you encounter problems with them then please consider installing `micro_sam` via [conda](#from-conda) instead.
-
-**Linux Installer:**
-
-To use the installer:
-- Unpack the you have downloaded.
-- Make the installer executable: `$ chmod +x micro_sam-0.2.0post1-Linux-x86_64.sh`
-- Run the installer: `$./micro_sam-0.2.0post1-Linux-x86_64.sh$` 
-    - You can select where to install `micro_sam` during the installation. By default it will be installed in `$HOME/micro_sam`.
-    - The installer will unpack all `micro_sam` files to the installation directory.
-- After the installation you can start the annotator with the command `.../micro_sam/bin/micro_sam.annotator`.
-    - To make it easier to run the annotation tool you can add `.../micro_sam/bin` to your `PATH` or set a softlink to `.../micro_sam/bin/micro_sam.annotator`.
-
-**Mac Installer:**
-
-To use the Mac installer you will need to enable installing unsigned applications. Please follow [the instructions for 'Disabling Gatekeeper for one application only' here](https://disable-gatekeeper.github.io/).
-<!---
-Alternative link on how to disable gatekeeper.
-https://www.makeuseof.com/how-to-disable-gatekeeper-mac/
--->
-
-TODO detailed instruction
-
-**Windows Installer:**
-
-TODO
 
 ## From source
 
@@ -105,3 +76,47 @@ $ pip install -e .
         - Install `micro_sam` by running `pip install -e .` in this folder.
     - **Note:** we have seen many issues with the pytorch installation on MAC. If a wrong pytorch version is installed for you (which will cause pytorch errors once you run the application) please try again with a clean `mambaforge` installation. Please install the `OS X, arm64` version from [here](https://github.com/conda-forge/miniforge#mambaforge).
     - Some MACs require a specific installation order of packages. If the steps layed out above don't work for you please check out the procedure described [in this github issue](https://github.com/computational-cell-analytics/micro-sam/issues/77).
+
+
+## From installer
+
+We also provide installers for Linuxand Windows:
+- [Linux](https://owncloud.gwdg.de/index.php/s/Cw9RmA3BlyqKJeU)
+- [Windows](https://owncloud.gwdg.de/index.php/s/1iD1eIcMZvEyE6d)
+<!---
+- [Mac](https://owncloud.gwdg.de/index.php/s/7YupGgACw9SHy2P)
+-->
+**The installers are stil experimental and not fully tested.** Mac is not supported yet, but we are working on also providing an installer for it.
+
+If you encounter problems with them then please consider installing `micro_sam` via [conda](#from-conda) instead.
+
+**Linux Installer:**
+
+To use the installer:
+- Unpack the zip file you have downloaded.
+- Make the installer executable: `$ chmod +x micro_sam-0.2.0post1-Linux-x86_64.sh`
+- Run the installer: `$./micro_sam-0.2.0post1-Linux-x86_64.sh$` 
+    - You can select where to install `micro_sam` during the installation. By default it will be installed in `$HOME/micro_sam`.
+    - The installer will unpack all `micro_sam` files to the installation directory.
+- After the installation you can start the annotator with the command `.../micro_sam/bin/micro_sam.annotator`.
+    - To make it easier to run the annotation tool you can add `.../micro_sam/bin` to your `PATH` or set a softlink to `.../micro_sam/bin/micro_sam.annotator`.
+
+<!---
+**Mac Installer:**
+
+To use the Mac installer you will need to enable installing unsigned applications. Please follow [the instructions for 'Disabling Gatekeeper for one application only' here](https://disable-gatekeeper.github.io/).
+
+Alternative link on how to disable gatekeeper.
+https://www.makeuseof.com/how-to-disable-gatekeeper-mac/
+
+TODO detailed instruction
+-->
+
+**Windows Installer:**
+
+- Unpack the zip file you have downloaded.
+- Run the installer by double clicking on it.
+- Choose installation type: `Just Me(recommended)` or `All Users(requires admin privileges)`.
+- Choose installation path. By default it will be installed in `C:\Users\<Username>\micro_sam` for `Just Me` installation or in `C:\ProgramData\micro_sam` for `All Users`.
+	- The installer will unpack all micro_sam files to the installation directory.
+- After the installation you can start the annotator by double clicking on `.\micro_sam\Scripts\micro_sam.annotator.exe` or  with the command `.\micro_sam\Scripts\micro_sam.annotator.exe` from the Command Prompt.