Fiji Connect Panel

Allows communication with Fiji. Requires Fiji to be installed, please refer to the System Requirements section for details. Fiji Connect uses MIJ , a Java package for bi-directional communication and data exchange from Matlab to ImageJ/Fiji, developed by Daniel Sage, Dimiter Prodanov, Jean-Yves Tinevez and Johannes Schindelin. This package should be integrated into Fiji.

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Video tutorial

Detailed demonstration on data exchange between MIB and Fiji can be seen in a video tutorial:
Visualization of datasets and models using Fiji

1. The Start Fiji button

Start an instance of Fiji by pressing this button. In order for communication between Matlab and Fiji to work, Fiji should be started from Matlab using this button. Press this button before doing anything else!

2. The Stop Fiji

After finishing work, Fiji may be stopped using this button. Press it at the end use of Fiji.

3. The Image Type combo box

The combo box defines type of the layer that should be exchanged with Fiji. For example, selection of the image entry in this menu allows to send the the currently opened image to Fiji after press of the Export button (4). See Example: Finding Edges using Fiji below for details.

4. The Export button

Press of this button sends the currently opened dataset (Image, Model, Mask, Selection, depending on settings in the Image type combo box 3) to Fiji.

5. The Import button

The Import button allows to transfer datasets from Fiji to MIB. The dataset can be imported as Image, Model, Mask, or Selection layer, set the distination using the Image Type combo box (3.). It is important that the size of the Model, Mask, Selection layers should match the size of the opened in MIB Image layer.

6. The Run macro edit box

It is possible to run a macro on Fiji. For that please type a macro command into this edit box. A template for the command is shown in the edit box by default. The command run('Flip Z') will Flip the Z-dimension of the selected in Fiji dataset. The execution of the macro is called by pressing the Run button (8).

The syntax for the macro command can be obtained from the corresponding reference page of Miji.

It is also possible to provide a list of macros in a filename in text format. In this case please enter a path to such file into this field. The file can be also selected using the Select file... button (7)

7. The Select file... button

It is possible to provide list of macro commands to use with Fiji. Press of this button allows selecting of such files. The execution of the script is done by pressing the Run button (8)

8. The Run button

Execute a macro written in the Run macro edit box (6). When edit box has a path to a text file with a set of macros the Run button loads that file and executes all the macros written in that script file.

9. The Help button

Access to the help page.

Example: Finding Edges using Fiji

Assuming that Fiji is installed and configured...

Let's try to use Fiji Find Edges function with a 3D grayscale dataset to find edges and generate a binary mask out of them. The test dataset can be obtained from here

  1. Open a dataset for tests
  2. Press the Start Fiji button to open an instance of Fiji
  3. If you want to send the opened image to Fiji, select image in the Image Type combo box and press the Export button
  4. In a appearing dialog enter name for the dataset to be used in Fiji
  5. Find edges: Fiji->Menu->Process->Find Edges
  6. Generate binary image from the edges: Fiji->Menu->Image->Adjust->Auto Threshold, set the Method to Mean, and check the Stack check box. Press OK to do thresholding
  7. In MIB select Fiji Connect->Image Type->mask and press the Import button
  8. Now MIB should have a new Mask layer imported from Fiji

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