How can I change current channel?

imagej
macro
channels

#1

In order to change colors (LUTs) of an image with 4 channels, I want to specify the current channel, so that I can specify an LUT for each channel.

Record functionality does not capture the change of the current channel. I could not find a command for this either in Python or JAVA or ImageJ macro. For example, IJ.run(imp, "Green", "") does not specify the target channel.

Can someone suggest a solution, please?


#2

Dear,

if a macro command is convenient, then please consult the list of commented macro commands

https://imagej.nih.gov/ij/developer/macro/functions.html

and especially:

Stack (hyperstack) Functions
These functions allow you to get and set the position (channel, slice and frame) of a hyperstack (a 4D or 5D stack). The HyperStackDemo demonstrates how to create a hyperstack and how to work with it using these functions

Stack.isHyperstack - Returns true if the current image is a hyperstack.
Stack.getDimensions(width, height, channels, slices, frames) Returns the dimensions of the current image.
Stack.setDimensions(channels, slices, frames) - Sets the 3rd, 4th and 5th dimensions of the current stack.
Stack.setChannel(n) - Displays channel n .
Stack.setSlice(n) - Displays slice n .
Stack.setFrame(n) - Displays frame n .
Stack.getPosition(channel, slice, frame) - Returns the current position.
Stack.setPosition(channel, slice, frame) - Sets the position.
Stack.getFrameRate() - Returns the frame rate (FPS).
Stack.setFrameRate(fps) - Sets the frame rate.
Stack.getFrameInterval() - Returns the frame interval in time (T) units.
Stack.setFrameInterval(interval) - Sets the frame interval in time (T) units.
Stack.getUnits(X, Y, Z, Time, Value) - Returns the x, y, z, time and value units.
Stack.setTUnit(string) - Sets the time unit.
Stack.setZUnit(string) - Sets the Z-dimension unit.
Stack.setDisplayMode(mode) - Sets the display mode, where mode is "composite", "color" or "grayscale". Requires a multi-channel stack and v1.40a or later.
Stack.getDisplayMode(mode) - Sets the string mode to the current display mode.
Stack.setActiveChannels(string) - Controls which channels in a composite color image are displayed, where string is a list of ones and zeros that specify the channels to display. For example, "101" causes channels 1 and 3 to be displayed.
Stack.getActiveChannels(string) - Returns a string that represents the state of the channels in a composite color image, where '1' indicates a displayed channel and '0' indicates an inactive channel.
Stack.swap(n1, n2) - Swaps the two specified stack images, where n1 and n2 are integers greater than 0 and less than or equal to nSlices.
Stack.getStatistics(voxelCount, mean, min, max, stdDev) - Calculates and returns stack statistics.
Stack.setOrthoViews(x, y, z) - If an Orthogonal Views is active, its crosspoint is set to x, y, z (example).
Stack.getOrthoViewsID - Returns the image ID of the current Orthogonal Views, or zero if none is active.
Stack.stopOrthoViews - Stops the current Orthogonal Views and closes the "YZ" and "XZ" windows. 

Regards

Herbie


#3

Thanks! I figured it out.

run("Make Composite");
Stack.setChannel(1);
run("Cyan");
Stack.setChannel(2);
run("Green");
Stack.setChannel(3);
run("Grays");
Stack.setChannel(4);
run("Magenta");

Is it harder with Python or Java then? Basically, I could not find an equivalent of Stack.setChannel(4);.


#4

It took me a couple of months to find this out. It’s all about documentation really.

As long as imp.isHyperStack() == 1, setC does the job.

imp = IJ.openImage("http://imagej.nih.gov/ij/images/Spindly-GFP.zip");
imp.show();
imp.setC(2); // set the current channel to 2

Also if the image has multiple slices, you can use imp.setSlice()

imp = IJ.openImage("http://imagej.nih.gov/ij/images/hela-cells.zip");
imp.show();
imp.setSlice(2);

#5

Good day,

what exactly do you mean by:

to change the channel

??

Did you have a look at:

public static ImagePlus run(ImagePlus img, int[] newOrder)

Changes the order of the channels in a hyperstack.

Parameters:
img - source hyperstack
newOrder - the new channel order
Returns:
a hyperstack with channels in the specified order

The following example opens the FluorescentCells sample image and reverses the order of the channels.
            ImagePlus img = IJ.openImage("http://imagej.nih.gov/ij/images/FluorescentCells.zip");
            int[] order = {3,2,1};
            ImagePlus img2 = ChannelArranger.run(img, order);
            img2.setDisplayMode(IJ.COLOR);
            img2.show();

Although it says

Changes the order of the channels in a hyperstack.

the above example uses not a hyperstack in the strict sense but a composite image!


#6

Thanks agian, I’ve messed it up a bit, but now the two methods above seem to be working.