Processing chains are the processing steps applied to a channel image to segment the objects of interest.
There are two types of processing chains:
- nucleus processing chains for segmentation of nuclei
- structure processing chains for segmentation of structures
Processing chains are composed of three successive steps:
- Pre-Filtering: Noise reduction, local contrasts enhancements, ...
- Segmentation: Labelling of objects.
- Post-Filtering: Correction of segmented objects, size exclusion, ...
Templates:
Templates are useful to re-use processing chains on several experiments.
It is easy to assign them to a structure. If the processing chain of the current structure is changed, the differences will be shown in blue (see "Choose template" for details).
Templates can be imported/exported, created from scratch, or from the processing chain of the current structure.
Templates can be created and edited in the "Structure Template" and "Nucleus Template" sub-tabs on the left.
Colors:
Buttons and parameters can appear in blue or red:
- red: the parameter is necessary and not filled correctly.
- blue: the parameter value is different from the template.
Current Structure
Processing chains of the structures of the current Experiment are edited in the "Current Structure" tab of the processing chain tab.
Choose Structure
Choose the structure of the current experiment to edit its template.
Choose Template
You can select an existing template.
Templates are useful to re-use processing chains on several experiments.
If you select a template, the current processing chain will be compared to the template.
When there is a difference in the number of elements (for pre/post filters) the add button is blue. When there is a difference in the value of a parameter, it is displayed in blue and the edit button of the element is also displayed in blue.
Copy From Template
Copies the selected template to the selected structure.
Copy To Template
Copies the current processing chain to the selected template.
Create New Template
Creates a new template with the current processing chain.
Test
Tests the current template on the corresponding structure of the first selected cell in the data tab.
Save
Saves all modifications made on processing chains.
Templates
TANGO also provides a template system with two main purposes:
- re-use a processing chain, to avoid creating them at each experiment. They can also be imported/exported.
- compare the current processing chain to a template: the differences with the template are highlighted in blue.
New
Creates a new processing chain. Names must be unique.
Rename
Renames the selected template. Caution: if the template is assigned to structures, you'll have to re-assign it.
Duplicate
Duplicates the selected template.
Remove
Removes the selected template.
Save
Saves changes on the selected template.
Define a sequence
A sequence is defined by three components :
- A pre-filtering component, usually to reduce noise and enhance structures of interest. This will create a new filtered image that will be used for segmentation.
- A segmentation procedure to detect the objects of interest. This will create a labelled image, with each object having its own value.
- A post-filtering component to improve the results of segmentation, usually some morphological filtering like opening or closing. Other plugins may include size discrimination or edge touching exclusion.
Pre-filtering
In this section you define the pre-filtering procedure (but you can leave it blank). Click Add and choose you pre-filter in the list (see the developer pages on how to create plugins for Tango).
Click on edit to edit the parameters of the selected method. See Processing and Quantification Modules.
Fast filters 3D
This set of filters allows you to perform 3D filtering on ellipsoidal neighbouring (different radii in XY and Z) in a parallel way (each processor will filter a set of slices). See Fast Filters 3D.
Segmentation
Select in this section the algorithm that will be used for segmentation. Click on edit to edit the parameters of the selected method. See Processing and Quantification Modules.
Post-filtering
In this section you define the post-filtering procedure (but you can leave it blank). Click Add and choose you pre-filter in the list (see the developer pages on how to create plugins for Tango).
Click on edit to edit the parameters of the selected method. See Processing and Quantification Modules.