fix nav issues in mkdocs.yml

docs/Scanner/tutorials/plant_3d_explorer.md

@@ -1,4 +1,4 @@
-How to use the ROMI `plant 3d explorer` to see your reconstructed and segmented plants ?
+How to use the ROMI `plant 3d explorer` to see the results generated from your plant phenotyping ?
 ================================
 
 ## Objective
@@ -9,44 +9,48 @@ After this tutorial, you should be able to:
 * explore the database content with the `Plant 3d explorer` menu page ;
 * For each plant, display, overlay and inspect in 3d every data generated during analysis
 
-## Prerequisite 
+## Prerequisite
 * install romi `plant 3d explorer` (from [source](https://github.com/romi/3d-plantviewer) or using a [docker image](../docker/plantviewer_docker.md) ) - read [install procedure](../install/plant3dexplorer_setup.md) 
 * install romi `plantdb` (from [source](https://github.com/romi/romidata) or using a [docker image](../docker/romidb_docker.md)) -- read [install procedure](../install/romidb_setup.md)
+* install romiscan / romirunner (for the Visualisation task -> to be done) 
 * Create and activate isolated python environment (see [here](/docs/Scanner/install/create_env.md) )
 
 ## Linked documentation
 * [Manual of the romi Plant 3d explorer](tobedone)
-* [How to install the romi plant 3d explorer](tobedone)
-* [Use docker compose to run both database and 3d explorer with docker](../docker/docker_compose.md)
 
 ## Step-by-step tutorial
 Principle: the `plant 3d explorer` is a web client that will display in your favorite web browser data exposed by a server (here, romi `plantdb`) on a particular url. The process consists in pointing the server to your folder of interest, start the server and start the client pointing on the served url. 
 
 !!! note: the `plant 3d explorer` has only been developed and tested on Chrome.
 
-### 1. Running a development server for the visualizer
+!!! note: if you prefer using docker only, skip steps 1. and 2. and readthe following procedure
+[Use docker compose to run both database and 3d explorer with docker containers](../docker/docker_compose.md)
 
-- Open a terminal 
-- ensure that the python environment (e.g. using ) required for romi command has been activated (or see this tutorial)
+### 1. Connect your database to a local server
 
-and set the DB location using the `DB_LOCATION` environment variable and launch the flask server:
+- Open a terminal 
+- if romi commands (like `romi_scanner_rest_api`) are not accessible from your terminal, activate the appropriate python environment (e.g. using venv or conda) required for romi commands (or [read this procedure](../install/create_env.md))
+- set the DB location using the `DB_LOCATION` environment variable and launch the flask server:
 ```bash
 export DB_LOCATION=/path/to/the/db
-romi_scanner_rest_api #comand that starts the server
+romi_scanner_rest_api #command that starts the server
 ```
-Finally, start the frontend visualization server (from `3d-plantviewer/` folder):
+### 2. Connect the `plant 3d explorer `to the server
+- Open a new terminal 
+- go to your local cloned directory of `3d-plantviewer/`
+- start the frontend visualization server by entering:
 ```bash
 npm start
 ```
-You should now be able to access the visualizer on [http://localhost:3000](http://localhost:3000).
+You should now be able to access the `plant 3d explorer` on [http://localhost:3000](http://localhost:3000). Depending on you system preferences, your default web browser may automatically open a window displaying teh server content. if not, open your web browser and enter [http://localhost:3000](http://localhost:3000) in the url bar.
 
 !!! note
     You need to add a file `.env.local` at project's root to set the API URL:
     ```REACT_APP_API_URL='{`API URL}'```
 
     Without this, the app will use: http://localhost:5000 which is the default for `romi_scanner_rest_api`.
 
-## Preparing your database
+### 2.  Preparing your database
 To access the data from your running DB (`` from ``)
 ```bash
 dataset_list=('2018-12-17_17-05-35' '2018-12-18_13-14-57' '2018-12-20_13-21-24' '2019-01-29_16-56-01' '2019-02-01_10-56-34')