Phriction Projects Wikis Bioimaging And Optics Platform Image Processing ImageJ/Fiji DEVILS ijp-devils History Version 3 vs 9
Version 3 vs 9
Version 3 vs 9
Edits
Edits
- Edit by romainGuiet, Version 9
- Apr 13 2018 16:24
- Edit by oburri, Version 3
- Apr 12 2018 08:29
| Edit Older Version 3... | Edit Current Version 9... |
Content Changes
Content Changes
Here you'll find some information about the plugin version of DEVILS.
=A.Install DEVILS=
**1.Download ** :
- using this link {F4607894}
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)
==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("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
{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 ==
{F7223405}
==5.Drag & Drop it on FIJI ==
{F4608012, size=full}
==6.Press {key 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.
{F4608018, size=full}
Here you'll find some information about the plugin version of DEVILS.
=A.Install DEVILS=
**1.Download ** :
- using this link {F4607894}
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)
==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- 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("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
{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 ==
{F7223405}
==5.Drag & Drop it on FIJI ==
{F4608012, size=full}
==6.Press {key 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.
{F4608018, size=full}
c4science · Help