Quantification and plotting
Explains the particle finder, functions for measuring particles, handling of result tables, and simple data plotting
Tutorial: Quantification and plotting
Load the example pipeline.
Processing compartment, disconnect the output node from the
Auto threshold 2D node (red arrow 1).
Locate the particle finder node by searching with keywords (red arrow 2, e.g., in the
Find matching algorithm window. Chose the
Find particles 2D node (red arrow 3) and add it to the pipeline (red arrow 4).
Find particles 2D node is the JIPipe equivalent of the ImageJ command
Analyze > Analyze Particles....
Find particles 2D node (red arrow 1) and examine the
Parameters tab (red arrow 2).
In addition to the name parameter (red arrow 3), the minimum and maximum values of the size and circularity (red arrows 4 to 7) can be controlled here, similarly to how it works in ImageJ.
Find particles 2D node (red arrow 1), preferable with
Cache intermediate results (red arrow 2). Examine the cache via the
Cache browser (red arrow 3).
The identified regions of interest are measured (red arrow 4) and the ROIs are also saved (red arrow 5).
Here 53 ROIs were found (column
String representation, red arrow 1), and they can be directly observed by double-clicking the cache item (red arrow 2).
Measurement table (red arrow 1) can be opened in a new window (red arrow 2) by double-clicking. The measured parameters are the same as provided in ImageJ (red rectangle 3), and we can also observe the annotations (red rectangle 4).
Many interfaces that can be opened by double-clicking entries in the cache browser allow to update the cache directly within the interface via the
Update cache button. By this way, you can track a specific result of interest while testing different parameters.
You can use the 📌 button to pin the window to the top.
Annotations sidebar can be hidden by clicking the button next to the 📌.
The table viewer (red arrow 1) provides additional functionalities (red rectangle), including saving the table as CSV or XLSX, applying a selection of functions, sending data to and from ImageJ results, etc.
In the table viewer (red arrow 1) it is also possible to plot column content. Click on the
Plot button (red arrow 2) and choose e.g., the
Histogram option (red arrow 3) .
Go to the
Series tab (red arrow 1) to select the source data. The name of the data series can be set (red arrow 2). Select e.g., the
Area column (red arrow 3).
The resulting histogram will appear, according to the default settings of its appearance.
To change the appearance of plots, go to the
Settings tab (red arrow 1), where the plot type can be changed (red arrow 2), together with many parameters (red arrow 3) as shown in the red rectangle 4.
These include, e.g., color schemes (red arrow 5), titles and labels (red arrow 6), font sizes and typefaces (red arrow 7), etc.
Experiment with these parameters!
It is always good practice to output the final results of a compartment into the compartment output.
Add a new input slot to the compartment output node for the ROI list (red arrow 1) by searching for
roi (red arrow 2) and selecting the
ROI list data type (red arrow 3).
Name the new slot (red arrow 4) and add it to the node (red arrow 5).
Add another input slot for
Measurements (use the search word “results” to find the
Results table data type) (red arrow 1).
Connect all three slots to the corresponding output slots (red arrows 2 to 4).
This completes this workflow.