Basic tutorials

Processing tables


Illustrates how to use some table processing capabilities included in JIPipe

Tutorial data

This tutorial has accompanying data. Please download the data if you want to follow the guide.

Preliminary steps

👉 This tutorial requires that you have installed node template Import images.

If you do not have these templates, you can download them via Manage > Download more templates or by importing the Templates.json file that is provided in the data package. If you do not know how to download or import node templates, please check out our tutorial.

Step 1

Create a new JIPipe project (red arrow 1) using a template (red arrow 2).

Step 2

Create a new JIPipe project (red arrow 1) using a template (red arrow 2).

Step 3

Locate the data folder that belongs to this tutorial (red arrow 1) and drop it on the UI (red arrow 2).

Click somewhere on the white area of the UI (red arrow 3) and chose the Node templates tab (red arrow 4).

Select the pre-made Import images template from the list (red arrow 5) and drag it to the UI. Connect it to the Folder list node (red arrow 6) and run the Import images node (red arrow 7.)

Step 4

The Cache browser (red arrow 1) will now show the fluorescence image (red arrow 2).

Step 5

Add the Basic blob finder template to the UI (red arrow 1) and observe the Parameters tab (red arrow 2).

The exposed parameter of the group node are indicated here (red rectangle 3), including the particle size and circularity ranges, the thresholding method and the gaussian smoothing factor.

Step 6

In order to observe the quality of the segmentation, add a Convert ROI to RGB node (red arrow 1), connect it to the ROI and Image outputs of the Import images and Basic blob finder nodes (red arrows 2 and 3), and run it (red arrow 4).

In the Cache browser (red arrow 5), observe the entry (red arrow 6) and the full image (red arrow 7).

Step 8

Before editing the table, find out the names of the measured parameters:

open the Measurements cache results of the Basic blob finder (red arrow 1), double-click on the cache entry (rectangle 2) and review the column names in the table viewer (rectangle 3).

Step 9

Let us calculate the ratio between the mean value and the area.

Select the Apply expression per row node (red arrow 1), open the Parameters tab and apply the following changes:

In parameter Expressions set the value of Expression to Mean / Area.

In parameter Expressions set the value of Column name to Density.

Step 10

Run the node (red arrow 1) and observe the Cache browser (red arrow 2).

The cache entry (red arrow 3) now contains a new Density column (red arrow 4).

Step 13

Run the node (red arrow 1) and observe the Cache (red arrow 2).

The new cache entry (red arrow 3) now contains the new column AVG density (red arrow 4, red rectangle 5).

Step 14

Finally, add three input nodes to the compartment’s output node and connect them accordingly. (red arrows 1-3).