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====== BMCR-Explorer ======


Terms of use: 


====== Explorer Tutorials ======

===== Tutorial 00: Adjusting sizes =====


{{youtube>EHzcN6A-Dyg?large&rel=0}}

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===== Tutorial 01: Basic controls =====


==== Mouse controls: ====

  * Explained in Tutorial 00
    * Mouse wheel to zoom in or out, hold the **"shift"** key to fast zoom. hold the  **"ctr"** key to inverse zooming direction

==== Keyboard controls: ====

  * Explained in Tutorial 00
    * **"a"** and **"d"** : previous or next slice
    * **"w"** and **"s"** : previous or next slice (fast)
    * **"space"** : switching focus between left and right hemisphere
  * Explained in Tutorial ?????
    * **"q"** and **"e"** : select an image for the top layer, or the layer beneath the top layer, respectively   
    * **"c"** show the focus center
    * **"1"** : <color white/rgb(75 94 68)> hide or show the background image</color>
    * **"2"**,**"3"** : <color white/rgb(71 99 102)>hide or show the image/annotation in the layer beneath the top layer (Background)</color>
    * **"4"**,**"5"** : <color white/rgb(122 88 92)>hide or show the image/annotation in the top layer (Overlay)</color>
    * **"6"**,**"7"** : <color white/rgb(115 115 115)>hide or show atlas information </color>


{{youtube>2c53PhORtc4?large&rel=0}}

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===== Tutorial 02: Opening data and using the flatmap navigation =====

{{youtube>bW0RDgmoz80?large&rel=0}}

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==== Acknowledgements ====

Voice has been generated using TTS (default parameters). https://github.com/mozilla/TTS


===== Nora-StackApp =====

The Nora-StackApp is based on the Nora medical imaging platform. Therefore, you might find the [[https://www.nora-imaging.org/doc/books/nora-documentation/page/first-steps|First Steps]] tutorial useful, too.

Basic keyboard and mouse controls:
  * Keep the left mouse button pressed while moving the cursor to navigate withing slices
  * Keep the right mouse button pressed while moving the cursor to shift a section
  * Use the mouse wheel to switch slices
  * Use the mouse wheel while keeping the control key pressed to zoom

You can also use the quick navigation menu as shown below:
<WRAP bia_inline_img>{{:tools:pasted:20230327-061144.png}}</WRAP>

==== Installation ====
Download a copy from the [[https://doi.org/10.60178/cbs.20230630-001|RIKEN CBS data portal]]. Select the NORA-StackApp folder as shown in the image below.
<WRAP bia_inline_img>{{:tools:pasted:20230327-044043.png}}</WRAP>

To download the StackApp, click on the {{:tools:pasted:20230327-044207.png?40x40}} symbol in the upper right corner.  It will open the download window (you might need to allow pop-up windows for the repository site). Below a screenshot of the download window: 

<WRAP bia_inline_img>{{:tools:pasted:20230327-044418.png?300}}</WRAP>

Please download the version for your OS (linux,mac or win). We have tested it on Ubuntu Linux, Windows 11 and an M1 Mac. Below a screenshot that illustrates how to run it from a Mac. Windows and Linux work in a similar way. You won't need to install the app, just unzip the folder. In the example below, we used the Desktop as destination. In a sub-folder of the unzipped folder, you will find the "Noraview" application (on Windows Noraview.exe). Starting it should bring up the main interface as shown below:

<WRAP bia_inline_img>{{tools:スクリーンショット_2023-03-26_21.08.43.png?400}}</WRAP>

The work-spaces menu provides several pre-defined work-spaces for marmosets.

<WRAP bia_inline_img>{{tools:スクリーンショット_2023-03-26_21.16.15.png?400}}</WRAP>

==== Download Tracer Data ====

When you download the Nora-StackApp, you already have the atlases and the template images that are used for the work-spaces. But you might want to download tracer data image stacks and additional atlases from the RIKEN CBS data repository:

  - Anterograde tracer data: "Volumetric_anterograde_tracer_data"
  - Retrograde tracer from the Marmoset Brain Connectivity Project
  - Atlases: Use the Nora-optimized versions under "STPT_reference_image_space" -> "Nora-StackApp_versions"

<WRAP bia_inline_img>{{:tools:pasted:20230327-053719.png?300}}{{:tools:pasted:20230327-055202.png?300}}</WRAP>

==== Marmoset Workspaces ====

The Nora-StackApp shows multiple 3D image stacks in a grid of views. Each view can show a section of an image. A view shows one main image  (e.g. a background image) and can have multiple "overlays". An overlay can be another image, such as a tracer signal, or an atlas. The example below shows the default marmoset workspace with two views, each showing a different slicing. It also shows the atlas tool. 

<WRAP bia_inline_img>{{:tools:pasted:20230327-052631.png}}</WRAP>

You can increase or decrease the number of views. Having more views can be helpful to show two different images side-by-side. Reducing the number of views gives a view more space on the screen.

<WRAP bia_inline_img>{{:tools:pasted:20230327-052700.png}}</WRAP>

The image below shows the default workspace, that shows our average template as background image. We have selected a nifti file with an anterograde tracer signal from our hard disk, and use the drag-and-drop feature of Nora to drop it into the first view as a new overlay. We then took the hand button of the tracer overlay and dropped it into the second view as well.

<WRAP bia_inline_img>{{:tools:pasted:20230327-052718.png}}</WRAP>

Open the BMCA-Explorer, and use the brain-symbol shown below, and drag and drop it into the explorer to set the current Explorer position to the same position as in Nora.

<WRAP bia_inline_img>{{:tools:pasted:20230327-052610.png?400}}</WRAP>

The video below shows a demonstration, including  interaction the with BMCA-Explorer:

 <WRAP bia_inline_video>{{youtube>RJ4ualdCweI?large&rel=0}}</WRAP>