Binary Options Stock Photos And Images - 123RF

counting pixels: threshold or make binary?

Hello, I am currently using imageJ to count pixels to determine %porosity. Is making the image binary enough for this purpose? Or should I adjust threshold (auto, default)? I'm getting different Area values from the two options above. Please and thank you!
submitted by marieieiel to ImageJ [link] [comments]

MakeOval Issues

*(PS: This is a repost from the ImageJ forums from me as well, but I just wanted to post here for a little more exposure. Wait times for replies on that forum kinda scared me!)
Hello!
I’m trying to analyze some samples (example image here: https://www.physicsforums.com/insights/wp-content/uploads/2015/09/tem.png), and everything seems to be working well except for the step where I am supposed to create four ovals in the area around the center of mass of the particles I am analyzing. Here is a part of the code:
open('https://www.physicsforums.com/insights/wp-content/uploads/2015/09/tem.png');
selectWindow("tem.png"); run("Set Scale...", "distance=468 known=2 pixel=1 unit=nm");
run("8-bit");
run("Duplicate...", " ");
run("Threshold...");
setAutoThreshold("Mean dark");
setOption("BlackBackground", false);
run("Convert to Mask");
//run("Despeckle");
//run("Make Binary");
//run("Erode");
//run("Erode");
//run("Minimum...", "radius=2");
run("Set Measurements...", "mean center limit add redirect=[tem.png] decimal=3");
run("Analyze Particles...", "size=1.5 circularity=0.2 pixel show=Nothing display clear add");
rad = getNumber("Input circle radius", 0);
numberOfPoints = getValue("results.count");
waitForUser("Start Data Analysis after this point:")
waitForUser(numberOfPoints)
//for (i = 0; i < numberOfPoints; i++) {
X = getResult("XM", i);
waitForUser(X);
Y = getResult("YM", i);
waitForUser(Y);
//setTool("oval");
waitForUser(rad);
waitForUser(X-(rad/2));
waitForUser(Y-(rad/2));
makeOval(X-(rad/2), Y-(rad/2), rad, rad);
roiManager("Add");
makeOval((X-(rad/2))+1, Y-(rad/2), rad, rad);
roiManager("Add");
makeOval((X-(rad/2))+1, (Y-(rad/2))+1, rad, rad);
roiManager("Add");
makeOval((X-(rad/2)), (Y-(rad/2))+1, rad, rad);
roiManager("Add");
//}
The problem I’m having is that the ovals appear in the top left corner of the image, even when I am certain that the program understands where the ovals should be. The program returns to me values that make sense for random particles but still puts the ovals in the top left corner. Any help here would be great.
Additionally, you should be able to run the code with that image and get to the step that I’m seeing, which is just a huge yellow region at the top left corner which if zoomed in you can see all the individual circles that were supposed to be over the particles. The strange thing is that this particular code works on simple images like a black and white polka dots image (I would recommend trying it with a white background and black dots), and the ovals are in the general area of where they are supposed to be. They are not perfect as the coordinates denote where the upper left corner of the bounding rectangle is, but it is certainly a start.
Thanks everyone.*
UPDATE: changed the code to "work" as it should. Thanks MurphysLab!!
open('https://www.physicsforums.com/insights/wp-content/uploads/2015/09/tem.png');
selectWindow("tem.png"); run("Set Scale...", "distance=468 known=2 pixel=1 unit=nm");
getPixelSize(unit, pixelWidth, pixelHeight)
waitForUser(pixelWidth);
waitForUser(pixelHeight);
run("8-bit");
run("Duplicate...", " ");
run("Threshold...");
setAutoThreshold("Mean dark");
setOption("BlackBackground", false);
run("Convert to Mask");
run("Despeckle");
run("Make Binary");
run("Erode");
run("Erode");
run("Minimum...", "radius=2");
run("Set Measurements...", "mean center limit add redirect=[tem.png] decimal=3");
//Rename redirect here
run("Analyze Particles...", "size=1.5 circularity=0.2 pixel show=Nothing display clear add"); //Change size of particle
rad = getNumber("Input circle radius", 0);
numberOfPoints = getValue("results.count");
waitForUser("Start Data Analysis after this point:")
waitForUser(numberOfPoints)
for (i = 0; i < numberOfPoints; i++) {
X = getResult("XM", i); //waitForUser(X); Y = getResult("YM", i); //waitForUser(Y); //setTool("oval"); //waitForUser(rad); //waitForUser(X-(rad/2)); //waitForUser(Y-(rad/2)); makeOval((**X/pixelWidth**)-(rad/2), (**Y/pixelHeight**)-(rad/2), rad, rad); roiManager("Add"); makeOval(((**X/pixelWidth**)-(rad/2))+1, (**Y/pixelHeight**)-(rad/2), rad, rad); roiManager("Add"); makeOval(((**X/pixelWidth**)-(rad/2))+1, ((**Y/pixelHeight**)-(rad/2))+1, rad, rad); roiManager("Add"); makeOval(((**X/pixelWidth**)-(rad/2)), ((**Y/pixelHeight**)-(rad/2))+1, rad, rad); roiManager("Add"); 
}
submitted by Lorundir to ImageJ [link] [comments]

Problem adding results to results table

So I had some help with this macro and I'm still fairly new to writing things for ImageJ. The code is some of my work and a bunch of stuff others have helped with. In general, I'm trying to analyze a bunch of thresholded/binary images with analyze particles to generate ROI in each image. Then, I would like to use the ROI and apply them to the original image, before it was thresholded, and analyze the texture of the objects within those ROI. This is done with the GLCM texture plugin. So far this works and I can get results for one ROI after another - each in a new results window. What I would like is for all the results to display one after the other so I can save it all in one file. I trued adding updateResults() to no avail.
print("start directory loop"); dir = getDirectory("Choose input segment Directory, the thresholded image folder"); // analyze particles will be run on these thresholded images to generate ROIs. list = getFileList(dir); // gives ImageJ a list of all files in the folder to work through print("number of files in dir1 Segments",list.length); // optional prints the number of files in the folder dir2 = getDirectory("Choose input Image Directory, the raw images "); // promts user to select folder to be saved in list2 = getFileList(dir2); // gives ImageJ a list of all files in the folder to work through for directory2 extension2 = ".tif"; //defines file type variable print("number of files in dir2 Image",list2.length); // optional prints the number of files in the folder dir3= getDirectory("Choose output Directory"); //promts user to select folder on Images for Results setBatchMode(true); // runs up to 6 times faster, without showing images onscreen. Turn off during troubleshooting steps?? dbugp = 1; //verbose print for debug // Note that the above processes are outside the loop brackets { }, // so they will only be called once at the beginning of the macro print("START..."); // main files loop // (process every image until you get to the bottom of the list) for (f=0; f0) { // optional prints the path & file name to a log window print("Name of path reading file from dir1",path); } showProgress(f, list.length); // optional progress monitor displayed at top of Fiji if(!endsWith(path,"/")) { open(path); } // if subdirectory, push down into it Still have to open Path /* if (nImages>=1) { // stop when there are no more open images */ t=getTitle(); // gets the name of the image being processed //add specific steps to create threshold and Roi run("Analyze Particles...", "display exclude include summarize add in_situ"); n=roiManager("count"); print("ROIi_number=" + n); //roiManager("Rename",tt+"roi"+n); if(roiManager("count")>0) { roiManager("Save", dir3 + t +"roi"+n +".zip"); for(i=0; i 
submitted by lostthesis to ImageJ [link] [comments]

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How to do Image Thresholding in ImageJ - YouTube

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