Questions tagged [imagej-macro]
89 questions
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ImageJ batch processing: saving results of each image separately in the csv format
I have around 30 images and use ImageJ macros to analyse the particles (area, circularity, etc.) in the batch. From the macros script that I'm using, I'm not able to save the results separately, I mean one results.csv file per…
user15877014
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How to detect a black frame using mean intensity and remove it from an avi file using imagej?
I want to build a plugin with fiji, where I input an avi video/frame sequences of grayscale and output the avi/frames with no black frames (remove them).
I though of recording a macro for that. I downloaded an avi video and imported the frames to…
Kenan Morani
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Setting up ImageJ Macros to batch process lab images
I'm currently trying to batch process a lot of lab images at once using ImageJ/Fiji but I'm having a hard time making it process the images. Whenever a file is pulled up, there are three images which are split into channels and open in separate…
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How to save the makeline information (coordinates) in Fiji (imageJ) which comes from the user
I have a macro in Fiji where I am using the waitForUser("For creating the plot", "Make a line along the diameter of the cell and press OK") code and I want to save the coordinates of the line drawn by user, can someone please help as to how this can…
Dhanlakshmi
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ImageJ/Fiji - Save CSV using macro
I am not a coder but trying to turn ThunderSTORM's batch process into an automated one where I have a single input folder and a single output folder.
input_directory = newArray("C:\\Users\\me\\Desktop\\Images");
output_directory =…
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Randomly generate points in an Image in a selected ROI. (Image J macro)
I am trying to put n dots randomly on a selected ROI in an image using the macro;
Roi.getBounds(x,y,w,h);
count = 0;
while (count < n) {
roiManager( "select", 0 ); // select the first, "big" ROI
x1 = random() * w + x;
y1 = random() * h…
user18310630
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Applying a System Call for ImageJ over a List in R
I am working with a large number of image files within several subdirectories of one parent folder.
I am attempting to run an ImageJ macro to batch-process the images (specifically, I am trying to stitch together a series of images taken on the…
Kelly N.
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how to repeat in Fiji
I was wondering if it is possible to write in into macro to repeat just a part of the macro in imageJ.
I have a code
selectWindow("Red");
run("Duplicate...", " ");
rename("Red-Dup");
run("8-bit");
run("Subtract...", "value=25");
run("Duplicate...",…
Severian
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Point selection in pictures with custom scale
I try to analyze images with Fiji. Therefore I first “calibrate” the scale with set scale run(“Set Scale…”, “distance=52.6 known=30 pixel=1 unit=no global”); and then make a rectangle as seen in the picture: Pic 1. Then I execute a measurement with…
maxgotstuck
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How to loop through each point of a multi point selection to get the pixel value?
I'm new to ImageJ and ImageJ macro. I started to make a macro that apply the "Find Maxima" function on an image. Then I would like to test each pixel spotted as maxima to filter them by value. How can I loop through all the points of the selection…
damien200
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Undefined variable error when running macro in ImageJ
I am new to ImageJ macros and I want to use a macro in Fiji. The code for the macro is from this source.
macro "MultiRoiMove Tool - C00cT0f16M" {
if (RoiManager.selected<2) exit();
…
ceno980
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Writing Macro in ImageJ to open, change color, adjust brightness and resave microscope images
I'm trying to write a code in Image J that will:
Open all images in separate windows that contains "488" within a folder
Use look up tables to convert images to green and RGB color From ImageJ, the commands are: run("Green"); and run("RGB…
AgatheB
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How to Install a toolset in Fiji or ImageJ
New to FIJI and ImageJ here, so I apologize if this question sounds idiotic to the veterans. I came across a really cool toolset that can deblur laser scanning microscopy images here: http://image.bio.methods.free.fr/lsmtrans.html but it is missing…
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How to write csv file from the results after some statistics using ImageJ macro?
After some image processing using ImgaeJ macro, I have a ‘Results’ tab which contains 2 columns A and B. Lets’s say I have 50 rows of data.
Now I want to subtract the value of last row from all other 49 rows above in column B.
After this, I want to…
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ImageJ: Ask input n times using Script Parameters?
I am trying to write a Macro in IJ1 which would ask the user:
the number of event they want to record
to name those events
I started using Script Parameters as follow:
// @ Integer (label="How many events do you want to record ?", min=1, max=50,…
Orohena
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