Create installation and usage instructions

README.md

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+# MedSAM-Lite 3D Slicer Plugin
+
+This is the official repository for 3D Slicer Plugin for MedSAM: Segment Anything in Medical Images.
+
+## Installation
+
+1. Install 3D Slicer from its official [website](https://download.slicer.org/). The compatibility of our plugin has been tested with 3D Slicer >= 5.4.0
+2. Download the specific version of the plugin from [releases](https://github.com/bowang-lab/MedSAMSlicer/releases) page and extract to your desired location.
+3. In the Slicer App, select the `Welcome to Slicer` drop-down menu in the toolbar at the top and navigate to `Developer Tools > Extension Wizard`.
+4. Click on `select Extension` and locate the `MedSAM` folder among the extracted files and directories at step 2. Accept if asked to add the new modules.
+5. Now, from the  `Welcome to Slicer` drop-down menu, under the `Segmentation` sub-menu, `MedSAMLite` option is added. By choosing it, you get to the final steps.
+6. Select a directory to download and install dependencies. It can take several minutes.
+7. Restart 3D Slicer.
+
+## Usage
+
+1. From the  `Welcome to Slicer` drop-down menu, under the `Segmentation` sub-menu, `MedSAMLite` option is added. By choosing it, you get to the final steps.
+2. Load your image file.
+3. From `Prepare Data` accordion menu you can choose from preset preprocessing methods (optional, but extremely helpful)
+4. From `Select the Region of Interest` accordion menu, you can click on `Attach ROI` to select the region for segmentation.
+5. From `Start Segmentation` accordion menu, click on `Send Image` button. It will send the whole 3D image to the backend of the module for process. It will take several minutes. You will need to do this step only once for each image. As long as the image is not changed (new preprocessing / cropping / etc.) you do not have to redo this step.
+	**Note For Windows Users**. At this step, firewall might stop the backend and ask for the permission. Grant the permission. In some cases you might need to reboot your computer to update permissions. 
+6. Click on `Segmentation` button to get the segmentation results. You can replace your ROI or delete and re-attach it (step 4) as many times as you need and repeat step 6 without going over step 5 again.
+7. In the same section, from the `Segmentation` and `Source volume` drop-down menus you can choose the right segmentation group and manually refine the segmentation results. You can also assign different color to each segmentation mask.