Home.md

@@ -150,7 +150,7 @@ Default positions | Example on how (sub)positions are imaged and named
  :---| :---
 <img src="./images/stage_positions.PNG" width = "400px"> |  <img src="./images/grid_subgrid.PNG" width = "200px" >
 
-** Explanations of the buttons**
+**Explanations of the buttons**
 1. **Single**: performs imaging at current stage position  
 2. **Multiple**: Imaging at multiple positions specified by the user using **Mark** (8).  
 3. **Grid**: Use a regularly spaced grid + subgrid. The first marked position sets the first point of the grid 
@@ -219,7 +219,7 @@ Start stop  | Explanations of the buttons
 <img src="./images/pipcon_startstop.PNG" width = "400px"> |  1. Start acquisition <br/> 2. Start acquisition and send commands to LabView water pump controller (optional) <br/> 3. Stop acquisition <br/> 4. Stop acquistion at the end of current repetition <br/> 5. Pause acquisition <br/> 6. Load pipelines settings from *PipelineConstructor.ini* file <br/>7. Save pipeline settings to a specific location <br/> 8. Show online image analysis registry keys
 
 
-# [<img src="./images/up.PNG">](#back) <a name="adaptivefeedback"></a> Adaptive Feeback Microscopy
+# [<img src="./images/up.PNG">](#back) <a name="adaptivefeedback"></a> Adaptive feedback microscopy/Online image analysis
 
 With the adaptive feedback microscopy capability the user can combine online image analysis and image acquisition and perform:
 * Detection of rare events and start a different imaging protocol
@@ -240,7 +240,7 @@ MyPiC communicates with external programs by reading and writing in the Windows
 HKEY_CURRENT_USER\Software\VB and VBA Program Settings\OnlineImageAnalysis\macro
 ```
 
-This occurs for each imaging job when *Online img. analysis* in the Method of [Processing and Tracking](#taskopt) is set. After the acquisition of the corresponding job the key [**CodeMic**](#codemic) will be set to `wait`, [**CodeOia**](#codeoia) to `newImage` and [**filePath**](#filepath)  to the name of image to analyze. MyPiC will continuously monitor **CodeMic** until the value changes from `wait` to one of the other possible values. If **CodeMic** is `focus`, `trigger1`, `trigger2` coordinates from keys [**X, Y, Z**](#xyz) and [**FCSX, FCSY, FCSZ**] are read. Via the registry we can also dynamically set bleaching or acquisition [ROIs](#rois) for an automated FRAP experiment. A list of online image analysis keys can be obtained by clicking on the ```Show OIA Keys``` button of the main Macro window.
+This occurs for each imaging job when **Online img. analysis** in the Method of [Processing and Tracking](#taskopt) is set. After the acquisition of the corresponding job the key [**CodeMic**](#codemic) will be set to `wait`, [**CodeOia**](#codeoia) to `newImage` and [**filePath**](#filepath)  to the name of image to analyze. MyPiC will continuously monitor **CodeMic** until the value changes from `wait` to one of the other possible values. If **CodeMic** is `focus`, `trigger1`, `trigger2` coordinates from keys [**X, Y, Z**](#xyz) and [**FCSX, FCSY, FCSZ**](#fcsxyz) are read. Via the registry the user can also dynamically set bleaching or acquisition [ROIs](#rois) for an automated FRAP experiment. A list of online image analysis keys can be obtained by clicking on the **Show OIA Keys** button of the main Macro window.
 
 <div align='center'>
 <img src="./images/windowsRegistryCommands.jpg" width = "600px">
@@ -291,6 +291,7 @@ Specifies stage positions. Coordinates with respect to upper left corner of the
 `Y1;Y2;Y3;...` | Y positions with respect to upper corner  in pixels
 `Z1;Z2;Z3;...`  | Z positions with respect to bottom slice in pixels. If this key is left empty current focus position is used.
 
+<a name="fcsxyz"></a>
 #### Keys **fcsX**, **fcsY**, **fcsZ**
 
 Specifies FCS scanner positions. Coordinates with respect to upper left corner of the image (in pixels) and first slice (0,0,0). Several points are separated by `;`