Here you'll find some information about the plugin version of DEVILS. =A.Install DEVILS= **1.Download ** : - using this link {F7204998} or - from c4science repository [[ https://c4science.ch/source/ijp-DEVIL/browse/master/target/DEVIL_-1.0.0-SNAPSHOT.jar | 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 {key 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) {F4607920, size=full} ==B.2. Advanced Mode == After selecting the file, you can activate the `Advanced Parameters` tick box {F4607923, size=full} It'll open a new window {F4607941, size=full} that will enable you to specifiy: - 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 ```lang=javascript selected_file = File.openDialog("Please select an image"); basicMode = false; if (basicMode){ // Basic largest_object_size = 25; run("DEVIL", "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("DEVIL", "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 {F4056415} - `jsr166y.jar` - Is the java library that GPARS depends on {F4056413} NOTE: We make use of [[http://www.gpars.org/ | GPARS: A Concurrency & Parallelism Framework]] to take advantage of the maximum possible performance of our workstations.We provide them here for convenience. If you want to make sure you have the latest versions, you can [[ http://groovy-lang.org/download.html | download and unzip Groovy ]] (Just get the binaries) and grab the 4 files from the `lib` folder. ==3.Restart Fiji== ==4.Download this groovy script == {F4608011} ==5.Drag & Drop it on FIJI == {F4608012, size=full} ==6.Press {key Run} == You shoulf 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. {F4608018, size=full}

Here you'll find some information about the plugin version of DEVILS. =A.Install DEVILS= **1.Download ** : - using this link {F7204998} or - from c4science repository [[ https://c4science.ch/source/ijp-DEVIL/browse/master/target/DEVIL_-1.0.0-SNAPSHOT.jar | 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 {key 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) {F4607920, size=full} ==B.2. Advanced Mode == After selecting the file, you can activate the `Advanced Parameters` tick box {F4607923, size=full} It'll open a new window {F4607941, size=full} that will enable you to specifiy: - 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 ```lang=javascript 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("DEVIL", "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 {F4056415} - `jsr166y.jar` - Is the java library that GPARS depends on {F4056413} NOTE: We make use of [[http://www.gpars.org/ | GPARS: A Concurrency & Parallelism Framework]] to take advantage of the maximum possible performance of our workstations.We provide them here for convenience. If you want to make sure you have the latest versions, you can [[ http://groovy-lang.org/download.html | download and unzip Groovy ]] (Just get the binaries) and grab the 4 files from the `lib` folder. ==3.Restart Fiji== ==4.Download this groovy script == {F4608011} ==5.Drag & Drop it on FIJI == {F4608012, size=full} ==6.Press {key Run} == You shoulf 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. {F4608018, size=full}

Here you'll find some information about the plugin version of DEVILS. =A.Install DEVILS= **1.Download ** : - using this link {F7204998} or - from c4science repository [[ https://c4science.ch/source/ijp-DEVIL/browse/master/target/DEVIL_-1.0.0-SNAPSHOT.jar | 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 {key 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) {F4607920, size=full} ==B.2. Advanced Mode == After selecting the file, you can activate the `Advanced Parameters` tick box {F4607923, size=full} It'll open a new window {F4607941, size=full} that will enable you to specifiy: - 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 ```lang=javascript 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("DEVIL", "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 {F4056415} - `jsr166y.jar` - Is the java library that GPARS depends on {F4056413} NOTE: We make use of [[http://www.gpars.org/ | GPARS: A Concurrency & Parallelism Framework]] to take advantage of the maximum possible performance of our workstations.We provide them here for convenience. If you want to make sure you have the latest versions, you can [[ http://groovy-lang.org/download.html | download and unzip Groovy ]] (Just get the binaries) and grab the 4 files from the `lib` folder. ==3.Restart Fiji== ==4.Download this groovy script == {F4608011} ==5.Drag & Drop it on FIJI == {F4608012, size=full} ==6.Press {key Run} == You shoulf 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. {F4608018, size=full}