ijp-devils

Updated 2,413 Days AgoPublic

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Here you'll find some information about the plugin version of DEVILS.

A.Install DEVILS

1.Download :

• using this link
  DEVILS_-1.0.1.jar16 KBDownload

or

• from c4science repository Download Raw File -> Download File

2.Add the jar file to Fiji>plugins

Restart Fiji, you will find the DEVIL in Plugins>BIOP>DEVIL

B.Run DEVILS

Plugins > BIOP > DEVILS

B.1. Basic Mode

Use Browse... to select your file on your hardrive
You should also specify the size of your largest object of interest in your image (in pixel)

B.2. Advanced Mode

After selecting the file, you can activate the Advanced Parameters tick box

It'll open a new window

• an output folder (leave it empty to use the default output folder)
• minimum and maximum intensity before rescaling (when you output 16-bit images)
• an object size (in pixel)
• the bit-depth of the output (either 16 ou 32)

Minimum and Maximum Intensity

These numbers represent the values that will correspond to 0 and 65535 respectively in the final image if converting the result from DEVILS from 32-bit to 16-bit.

B.3. Macro Language Mode

Please find here a exemple script in macro language to use DEVIL in Basic or Advanced mode

selected_file = File.openDialog("Please select an image");

basicMode = false;
if (basicMode){
	// Basic
	largest_object_size = 25;
	run("DEVILS", "select_file=["+selected_file+"] largest_object_size=["+largest_object_size+"]");

}else{
	//
	output_directory = getDirectory("Please select an Output folder") ;
	// Advanced parameters
	minimumChannel_string 	= "-100,-2,-10";
	maximumChannel_string 	= "10000,20000,5000";
	objectSize_string 		= "5,15,20";
	bitDepth_string 		= "16";
	
	run("DEVILS", 	"select_file=["+selected_file+"] largest_object_size=25"+ 
					" advanced_parameters"+
					" output_directory="+output_directory+
					" minimum=["+minimumChannel_string+"]"+
					" maximum=["+maximumChannel_string+"]"+
					" object=["+objectSize_string+"]"+
					" output_bit_depth="+bitDepth_string+"-bit");
}

C. Run Parallele DEVILS using a groovy script

1.Install DEVILS in FIJI

(cf A.Install DEVIL)

2.Add the following "jar" files

To the folder Fiji/jars (not the Fiji/plugins nor the Fiji/plugins/jars !)

• gpars.jar - Is the concurrency framework that allows us to have fun with parallel loops

• jsr166y.jar - Is the java library that GPARS depends on

3.Restart Fiji

4.Download this groovy script

5.Drag & Drop it on FIJI

6.Press Run

You should see some Task starting in the task manager, some folders appearing and files being generated within these folders.

NOTE: If the script stops without errors or bugs appearing You may have to decrease the number of threads.