# Fiji ( Fiji Is Just ImageJ )

### Download

Go to the official site and download the version that works on your current operational system (Windows, Mac or Linux). It requires Java. Please upgrade to the latest version.

{% hint style="info" %}
<https://imagej.net/Fiji/Downloads>
{% endhint %}

####

### Open Fiji

#### On your personal computer.

The location of the executable may vary depending on the fiji version you are going to use. For version 2020, double click on:

```
path_to_fiji_folder/Fiji.app/ImajeJ-Windows64
or
path_to_fiji_folder/Fiji.app/ImajeJ-Linux64
or
path_to_fiji_folder/Fiji.app/ImajeJ-MacOs
```

#### On Oscar

Applications that require a graphics UI  ( window  ) needs a visual/interactive interface to work with. If you want to use the installed version of Fiji in Oscar you have to open a VNC session.

1. &#x20;Go to <https://web1.ccv.brown.edu/technologies/vnc> and download [CCV VNC client 2.0.2](https://brownbox.brown.edu/download.php?hash=fe8b9a93)
2. Doble click on the CCV\_VNC\_2.0.1.jar

![](https://1564297567-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2Fvisualization%2F-Lvp_Pf44BxRytdyT8T3%2F-Lvp_xXjfCLRzSYuurOs%2F0.png?generation=1576078400633552\&alt=media)

1. Use your ccv user and password (usually are the same brown credentials)
2. In the following pop up window select the last option ( 3 Cores - 15 GB Memory 2 GPU) and click on ‘Create VNC Session’’

![](https://1564297567-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2Fvisualization%2F-Lvp_Pf44BxRytdyT8T3%2F-Lvp_xXkHbG2Dr-u0M-5%2F1.png?generation=1576078400653497\&alt=media)

&#x20;Wait a few seconds (at least 60 seconds) to get the virtual desktop

![](https://1564297567-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2Fvisualization%2F-Lvp_Pf44BxRytdyT8T3%2F-Lvp_xXlYSfLy1VwNjEw%2F2.png?generation=1576078400654914\&alt=media)

**Opening Fiji UI**

1. Open terminal: Applications - > Utilities -> Terminal (this might differ depending on the Operating System UI)
2. Run the command

$ module load fiji/2020

&#x20; 3\. Run the command

$ ImageJ-linux64

You will see the Fiji Window

![](https://1564297567-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LvpZTppa56OvfLm71ut%2F-MCxZmXC-RPGpJ9Trxq_%2F-MCx_BgnBtNT_WGJRMBH%2Fimage.png?alt=media\&token=9585a994-df00-4b58-9bd2-fb416b52e1f9)

### Tutorials

For instructions on how to use the basic functionalities please follow the guide at:

```
https://imagej.net/Learn
```

Also, You can follow this video playlist from the Melbourne Advanced Microscopy Facility.

```
https://www.youtube.com/watch?v=1ZR3eztlvLo&list=PLvHJ_gpVJo-S9VIkZ7XJIYll3zpQoL0L7
```

### Data Examples

Fiji has a list of data samples you can play with. They are located at.

```
https://imagej.nih.gov/ij/images/
```