documentation updates

Author: haesleinhuepf

generate_clijx_plugins.md

@@ -7,12 +7,11 @@ directory of their Fiji installation.
 If you're about to generate Fiji plugins for the first time, please follow the installation instructions [here](https://clij.github.io/assistant/installation#maven) first.
 
 ## How does it work?
-After entering some parameters, such as plugin name, description, author and maven/java/git installation folders, a template is downloaded from here:
-https://github.com/clij/clijx-assistant-plugin-generator-template
+After entering some parameters, such as plugin name, description, author and maven/java/git installation folders, a template is downloaded from [here](https://github.com/clij/clijx-assistant-plugin-generator-template).
 Afterwards, some placeholders in this [ImageJ/Fiji/CLIJ maven project](https://imagej.net/Maven) are replaced before it is compiled and the resulting .jar file is installed to your Fijis `/plugins/` folder.
 
-<iframe src="images/generate_clijx_plugins3_acc.mp4" width="600" height="300"></iframe>
-[Download video](images/generate_clijx_plugins3_acc.mp4) 
+<iframe src="images/fiji_plugin_generator.mp4" width="600" height="300"></iframe>
+[Download video](images/fiji_plugin_generator.mp4) 
 
 Back to [CLIJx-Assistant](https://clij.github.io/assistant)
 

getting_started.md

@@ -29,10 +29,9 @@ You can use ImageJs `Duplicate...` menu or the built in menu:
 
 ![Image](images/interoperability_imagej.png)
 
-
 ## The assistant in action
-<iframe src="images/window_positioning.mp4" width="540" height="540"></iframe>
-[Download video](images/window_positioning.mp4)
+<iframe src="images/basic_usage.mp4" width="600" height="300"></iframe>
+[Download video](images/basic_usage.mp4)
 
 
 Back to [CLIJx-Assistant](https://clij.github.io/assistant)

icy_protocol_export.md

@@ -0,0 +1,15 @@
+# Intensity projection
+Workflows can be exported as Icy Protocols.
+
+## Installation
+If you want to conveniently open Icy Protocols directly from Fiji, 
+please follow the corresponding [installation instructions](https://clij.github.io/assistant/installation#icy).
+
+## Usage
+In order to export a workflow as protocol to Icy, click the right mouse button on any
+assistant window and click the menu `Generate Script > Icy Protocol`.
+
+Please note: Export to Icy Workflows is limited to operations from the CLIJ2 library at the moment.
+
+<iframe src="images/icy_export.mp4" width="600" height="300"></iframe>
+[Download video](images/icy_export.mp4) 

images/basic_usage.mp4

@@ -5,14 +5,14 @@ Assuming one wants to analyse distances of cells towards a common structures suc
 ![Image](images/morpholibj_distance_map.png)
 
 ### Installation
-Activate the "IJPB-plugins" update site in Fiji.
+In order to use the MorphoLibJ extension, please follow the corresponding [installation instructions](https://clij.github.io/assistant/installation#extensions).
 
 ### Application
  * Starting point: Intensity image showing nuclei 
    * Threshold Otsu 
      * Connected Components Labeling 
        * Pull To ROIManager 
- * Starting point: Binary image representing vessels... 
+ * Starting point: Binary image representing vessels for example
    * Binary Not 
      * Morpho Lib J Chamfer Distance Map 
 

images/fiji_plugin_generator.mp4

@@ -1,12 +1,4 @@
-# Parameter optimization
-
----
-Note: Parameter optimization is deactivated at the moment for technical reasons. Stay tuned.
----
-
-
-
-
+# Parameter optimization for binarization operations
 If a workflow results in a binary image and some annotations are availabe, its parameters can be automatically optimized.
 To prepare the optimization, draw Freehand or Polyline ROIs and store them in the ROI Manager. 
 Name the positive annotations "p" and the negative annotations "n" (background).

images/generate_clijx_plugins.mp4

@@ -1,13 +1,13 @@
 # CLIJx-Assistant
 [CLIJx-Assistant](https://clij.github.io/assistant) is an intuitive user interface for building custom GPU-accelerated image processing workflows using [CLIJ2](https://clij.github.io) in [Fiji](https://fiji.sc). 
-It visualizes workflows while building them, suggests what to do next and generates scripts and human readable protocols to facilitate reproducible bio-image analysis. 
-These generated scripts also run in other platforms such as Matlab, Icy, Python and QuPath.
+It visualizes workflows as image date flow graphs while building them. 
+It suggests what to do next and generates scripts and human readable protocols to facilitate reproducible bio-image analysis. 
+These generated scripts also be executed in other platforms such as Matlab, Icy, Python and QuPath.
 
 CLIJx-Assistant is under development and is subject to change. 
-Please treat everything with care.
-Do not use it for routine research yet. 
-Planned release is early 2021. 
-Stay tuned.
+Give it a try and let us know what you think!
+Do not use it for routine research yet.  
+Provide feedback and stay tuned.
 
 <iframe src="images/clijxa_teaser1_fast.mp4" width="800" height="640"></iframe>
 [Download slower version of the video](images/clijxa_teaser1.mp4) [Image data source: Daniela Vorkel, Myers lab, CSBD / MPI CBG]
@@ -17,9 +17,7 @@ Stay tuned.
   * [Installation](https://clij.github.io/assistant/installation)
   * [Building workflows](https://clij.github.io/assistant/getting_started)
   * [Saving and loading workflows](https://clij.github.io/assistant/save_and_load)
-  * [Optimize parameters](https://clij.github.io/assistant/parameter_optimization)
   * [Undo parameter changes](https://clij.github.io/assistant/undo)
-  * [Reference](https://clij.github.io/assistant/reference)
 
 * Filtering / correction
   * [Image filtering](https://clij.github.io/assistant/filtering)
@@ -33,11 +31,10 @@ Stay tuned.
   * [Sphere projection](https://clij.github.io/assistant/sphere_projection)
 
 * Regionalisation
-  * Spot detection
-  * Cell segmentation
-    * [Nuclei segmentation](https://clij.github.io/assistant/segmentation_nuclei)
-    * [Cell segmentation based on membranes](https://clij.github.io/assistant/segmentation_cells)
-    * [Pixel classifier (Weka)](https://clij.github.io/assistant/clijx_weka_pixel_classifier)
+  * [Nuclei segmentation](https://clij.github.io/assistant/segmentation_nuclei)
+  * [Cell segmentation based on membranes](https://clij.github.io/assistant/segmentation_cells)
+  * [Optimize parameters for binarization](https://clij.github.io/assistant/parameter_optimization)
+  * [Pixel classifier (Weka)](https://clij.github.io/assistant/clijx_weka_pixel_classifier)
 
 * Analysis
   * [Cell neighbor analysis](https://clij.github.io/assistant/neighbor_analysis_generated)
@@ -46,20 +43,23 @@ Stay tuned.
 
 * Reproducibility / interoperability
   * [Export workflows as ImageJ Script](https://clij.github.io/assistant/macro_export)
-  * [Supplementary methods section generator](https://clij.github.io/assistant/supplementary_methods_section_generator)
+  * [Export human readable protocols and ImageJ Macro Markdown notebooks](https://clij.github.io/assistant/supplementary_methods_section_generator)
   * [Generate CLIJx / Fiji plugins](https://clij.github.io/assistant/generate_clijx_plugins)
+  * [Export as Icy Protocol](https://clij.github.io/assistant/icy_protocol_export)
   * [Export Groovy Script for QuPath](https://clij.github.io/assistant/export_to_clupath)
   * [Export workflows as Python script using clEsperanto and Napari](https://clij.github.io/assistant/te_oki_export)
 
+* [Reference](https://clij.github.io/assistant/reference)
+
 * Extensibility
   * [CLIJ2 Plugin template](https://github.com/clij/clij2-plugin-template)
-  * [CLIJ2 imglib2 example plugin](https://github.com/clij/clijx-assistant-imglib2)
-  * [CLIJ2 ImageJ example plugin](https://github.com/clij/clijx-assistant-imagej)
-  * [CLIJ2 ImageJ2 example plugin](https://github.com/clij/clijx-assistant-imagej2)
-  * [CLIJ2 BoneJ example plugin](https://github.com/clij/clijx-assistant-bonej)
-  * [CLIJ2 MorphoLibJ example plugin](https://github.com/clij/clijx-assistant-morpholibj)
-  * [CLIJ2 ImageJ 3D Suite example plugin](https://github.com/clij/clijx-assistant-imagej3dsuite)
-  * [CLIJ2 SimpleITK example plugin](https://github.com/clij/clijx-assistant-simpleitk)
+  * [CLIJ2 imglib2 extensions](https://github.com/clij/clijx-assistant-imglib2)
+  * [CLIJ2 ImageJ extensions](https://github.com/clij/clijx-assistant-imagej)
+  * [CLIJ2 ImageJ2 extensions](https://github.com/clij/clijx-assistant-imagej2)
+  * [CLIJ2 BoneJ extensions](https://github.com/clij/clijx-assistant-bonej)
+  * [CLIJ2 MorphoLibJ extensions](https://github.com/clij/clijx-assistant-morpholibj)
+  * [CLIJ2 ImageJ 3D Suite extensions](https://github.com/clij/clijx-assistant-imagej3dsuite)
+  * [CLIJ2 SimpleITK extensions](https://github.com/clij/clijx-assistant-simpleitk)
 
 ## Feedback welcome!
 I'm eager to receiving feedback: rhaase at mpi minus cbg dot de

images/generate_clijx_plugins3_acc.mp4

@@ -1,4 +1,4 @@
-## Supplementary Methods Section generator
+## Export human readable protocols
 Just like [generating scripts](https://clij.github.io/assistant/macro_export), one can also
 generate human readable protocols of workflows. Just click the right-click menu `Generate Script > Human readable protocol`.