👉 This tutorial requires that you have installed two node templates
Split channels: three channels, R, G, B order and
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.
Create a new JIPipe project (red arrow 1) using a template (red arrow 2).
Chose a template with one compartment.
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 choose 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 via the
Update cache command (red arrow 7.)
Cache browser (red arrow 1) will now show the fluorescence image (red arrow 2).
Next navigate to the
Node templates tab (red arrow 1) and drag the
Split channels: three channels R, G, B order template (red arrow 2) onto the graph.
Connect the newly created node to the output of
We will now apply a look-up table (LUT) to one of the channels.
To do this, use the search bar (red arrow 1) to add the following nodes:
Set LUT (color map)(red arrow 3)
Apply LUT(red arrow 2)
Connect the input of
Set LUT (color map) node to the
Red output of
Split channels: three channels R, G, B order.
Then connect the output of
Set LUT (color map) to the input of
Set LUT (color map) sets the image LUT to a predefined color map. There are also alternative options that generate LUT via two color parameters or apply the LUT from an 1×256 image.
Set LUT (color map) node (red arrow 1) and go to the Parameters tab (red arrow 2). Proceed to and activate the
Color map field (red arrow 3).
Select value window (red arrow 4), chose the desired look-up table, e.g.
Viridis (red arrow 5).
To change the pixel size and other physical dimensions of an image, search for nodes with the keyword
physical (red arrow 1). Select the
Set physical dimensions node (red arrow 2).
Drag the new node to the UI (red arrow 1) and connect it to, e.g., the
Green channel of the
Split channels node (red arrow 2).
Parameters menu (red arrow 3), enable the physical dimensions that need to be changed (red arrows 4, 5).
From the drop-down list (red arrow 6) choose the proper dimensions (red arrows 7, 8). The values can be entered in the neighboring fields (red arrows 9, 10).
For this example, set X and Y pixel dimensions both to 1.0 micrometer (
Read out the physical dimensions of the newly calibrated image by adding a node
Annotate with image properties (red arrow 1) and connecting it to the output of
Set physical dimensions.
Run the node and observe the
Cache browser (red arrow 2). Now both the X and Y dimensions are added to the annotations table (red arrows 3 and 4).