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plugin:utilities:tapas_tutorial:create_your_processing_pipeline:start [2019/04/19 06:40]
admin created
plugin:utilities:tapas_tutorial:create_your_processing_pipeline:start [2019/09/11 05:30] (current)
tboudier
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 This window will list all the available modules from the file //​tapas.txt//​ located in the ImageJ folder. When a module is selected, the available parameters are displayed on the right. If default values exist for these parameters they will be displayed. A short description of the selected module is also available below the list of modules. This window will list all the available modules from the file //​tapas.txt//​ located in the ImageJ folder. When a module is selected, the available parameters are displayed on the right. If default values exist for these parameters they will be displayed. A short description of the selected module is also available below the list of modules.
  
-The first module should always be input module, to load data from OMERO or a folder (please have a look to this [[plugin:​utilities:​tapas_tutorial_:​input_output_i:​start|tutorial on Input/​Output]]). ​+The first module should always be an input module, to load data from OMERO or a folder (please have a look to this [[plugin:​utilities:​tapas_tutorial_:​input_output_i:​start|tutorial on Input/​Output]]). ​
  
-In this tutorial we will start by **denoising** the image by using a 3D median filter. Select the module **3dfilters** (this should be the first available module). This module has parameters, the radii in X,Y and Z and the name of the filter. A list of modules with description of parameters is available {{:​plugin:​stacks:​3d_ij_suite:​tapasdescription.pdf|here}}. You can change parameters if you want, the list of available parameters are : median, mean, tophat, open, close, min and max. Then just click on **create text** to export ​the corresponding text for this module, in our case it is simply :+In this tutorial we will start by **denoising** the image by using a 3D median filter. Select the module **filters**. This module has parameters, the radius ​in XYradius in Z and the name of the filter. A list of modules with description of parameters is available {{:​plugin:​stacks:​3d_ij_suite:​tapasdescription.pdf|here}}. You can change parameters if you want, the list of available parameters are : median, mean, tophat, open, close, min and max. Then just click on **create text** to create ​the corresponding text for this module, in our case it is simply :
 <​code>​ <​code>​
-process:3dfilters +process:filters 
-radx:2 +radxy:2
-rady:2+
 radz:1 radz:1
 filter:​median filter:​median
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 {{:​plugin:​stacks:​3d_ij_suite:​menu2.png?​500|The first processing}} {{:​plugin:​stacks:​3d_ij_suite:​menu2.png?​500|The first processing}}
  
-There is no specific order for parameters. Note also that only parameters with modified or required values are to be explicitly entered; parameters with default values, if they exist, do not need to be entered, they can be omitted if you do not modify them, a short version of **3dfilters** is then :+There is no specific order for parameters. Note also that only parameters with modified or required values are to be explicitly entered; parameters with default values, if they exist, do not need to be entered, they can be omitted if you do not modify them, a short version of **filters** is then :
 <​code>​ <​code>​
 +// use the module filters with default values
 process:​3dfilters process:​3dfilters
 </​code> ​ </​code> ​
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 If you modify the filter but not the default radii, the text is then : If you modify the filter but not the default radii, the text is then :
 <​code>​ <​code>​
-process:3dfilters+process:filters
 filter:mean filter:mean
 </​code>​ </​code>​
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 If all parameters are modified they need to be entered : If all parameters are modified they need to be entered :
 <​code>​ <​code>​
-process:3dfilters+process:filters
 filter:mean filter:mean
-radx:4 +radxy:4
-rady:4+
 radz:2 radz:2
 </​code>​ </​code>​
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 First use the module **3dfilter** as seen above : First use the module **3dfilter** as seen above :
 <​code>​ <​code>​
-process:3dfilters +process:filters 
-radx:2 +radxy:2
-rady:2+
 radz:1 radz:1
 filter:​median filter:​median
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 </​code>​ </​code>​
  
-The image is now labeled, where the value of the pixel is the object number. The final module is **measurement**,​ it will perform geometric measurement of the objects present in the image. The **list** of available measurements are : volume, area, centroid, compactness,​ ellipsoid, DC (Distance to Center). Simply enter the name of the measurements separated by **,**. The measurements result will be saved as csv file (that you can opened ​with a spreadsheet software or with ImageJ). You will need to indicate the **directory** and the **file name** where to save this file. +The image is now labeled, where the value of the pixel is the object number. The final module is **measurement**,​ it will perform geometric measurement of the objects present in the image. The **list** of available measurements are : volume, area, centroid, compactness,​ ellipsoid, DC (Distance to Center). Simply enter the name of the measurements separated by **,**. The measurements result will be saved as csv file (that you can open with a spreadsheet software or with ImageJ). You will need to indicate the **directory** and the **file name** where to save this file. 
-By default the name of the file will be //​results.csv//​ and the directory will be the home directory using the keyword //?​home?//​.  ​+By defaultthe name of the file will be //​results.csv//​ and the directory will be the home directory using the keyword //?​home?//​.  ​
  
 Possible keywords for folders are : Possible keywords for folders are :
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 </​code>​ </​code>​
  
-By pressing each time of the create text button, you should obtain a complete processing pipeline text.+By pressing each time the// create text// button, you should obtain a complete processing pipeline text.
  
 {{:​plugin:​stacks:​3d_ij_suite:​menu3.png?​500|The final processing}} {{:​plugin:​stacks:​3d_ij_suite:​menu3.png?​500|The final processing}}
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 In case you have OMERO installed and want to push back the results into OMERO, you can use the module **attach**. First, you need to indicate which file you want to push back, by specifying its **directory** (//dir//) and its **file name** (//file//). Then you want to indicate which image in OMERO this file should be attached to, you need to specify the //​project//,​ //dataset// and //name// of the image. By default, the module will attach the file to the current processed image. ​ In case you have OMERO installed and want to push back the results into OMERO, you can use the module **attach**. First, you need to indicate which file you want to push back, by specifying its **directory** (//dir//) and its **file name** (//file//). Then you want to indicate which image in OMERO this file should be attached to, you need to specify the //​project//,​ //dataset// and //name// of the image. By default, the module will attach the file to the current processed image. ​
  
-The keyword //?​project?//​ corresponds to the project name of the currently processed image, similarly //?​dataset?//​ corresponds to the dataset name of the currently processed image and ?name? to the name of the currently processed image. The keywords can be coupled with static text, for example if all the results are saved in an another dataset called the name of the dataset followed by //​-results//,​ then we simply indicate //?​dataset?​-results//​. Note that in case you are using **TAPAS FILES**, the file wil lbe copied to the folder corresponding to the dataset. ​+The keyword //?​project?//​ corresponds to the project name of the currently processed image, similarly //?​dataset?//​ corresponds to the dataset name of the currently processed image and ?name? to the name of the currently processed image. The keywords can be coupled with static text, for example if all the results are saved in another dataset called the name of the original ​dataset followed by //​-results//,​ then we simply indicate //?​dataset?​-results//​. Note that in case you are using **TAPAS FILES**, the file will be copied to the folder corresponding to the dataset. ​
  
 We should obtain, in case we simply attach the results to the original image : We should obtain, in case we simply attach the results to the original image :
plugin/utilities/tapas_tutorial/create_your_processing_pipeline/start.txt · Last modified: 2019/09/11 05:30 by tboudier