Automation of ImageJ using Macros and Batch Processing

Please forgive the poor audio quality - I only had access to my laptop's in-built microphone at the time of recording.

[marc-andresparke]

Hi,
nice straight forward video! The problem I am encountering is that I do not get the nice summary table at the end! If I add the summary function it gives me a summary at the end of each image processing step, but it does not "summarize" them. U have an idea what I need to change?

[arjunsapkota]

Thank you for the video Arjun, I tried to analyse the mean grey scale value of the brain tissue.

I recorded my macro as follow

run("Color Threshold...");
// Color Thresholder 1.50i
// Autogenerated macro, single images only!
min=newArray(3);
max=newArray(3);
filter=newArray(3);
a=getTitle();
run("HSB Stack");
run("Convert Stack to Images");
selectWindow("Hue");
rename("0");
selectWindow("Saturation");
rename("1");
selectWindow("Brightness");
rename("2");
min[0]=0;
max[0]=255;
filter[0]="pass";
min[1]=0;
max[1]=255;
filter[1]="pass";
min[2]=114;
max[2]=255;
filter[2]="pass";
for (i=0;i<3;i++){
selectWindow(""+i);
setThreshold(min[i], max[i]);
run("Convert to Mask");
if (filter[i]=="stop") run("Invert");
}
imageCalculator("AND create", "0", "1");
imageCalculator("AND create", "Result of 0", "2");
for (i=0;i<3;i++){
selectWindow(""+i);
close();
}
selectWindow("Result of 0");
close();
selectWindow("Result of Result of 0");
rename(a);
// Colour
run("Measure");
run("Select All");


but when I run the macro result is not same as mannually operated result

[JovanWong]

very useful video, thanks for sharing!!

[genevievehuard]

Wow ! Wonderfull, thank you and your tutorial is perfect !

[yeefangxiao]

Thank you so much for the tutorial document. It helps me a lot!

[vengateshwaran]

I m currently doing project on nanoparticles synthesis . I collected sem, edx data, next how can i interpret the result like wheather it has succesfully synthesised the nano particles or not

[pedrofran]

Hi Arjun. Great tutorial, it definitively simplifies everything.

Quick question, I am trying to do the same on some raw images and their format is .bin.Unfortunately when I run the macros it shows a message like this "openImage() and openUsingBioFormats() returned null:..." .Is there any reason why this is happening?. I will really appreciate your help.

Thanks

[christinaparkes]

Quick Question. How once you have split your channels for an image in ImageJ. how do you choose to select one of those windows, and have the rest of the steps in the macro work on this window? I know how to do it for one, but I am trying to make a batch process of the whole thing? Any help would be greatly appreciated.

[SCRDan]

Hello, Arjun. First, thanks for the video. I would like to ask for a little advise. So, I'm trying to create a macro (code bellow), it's a pretty easy, straight forward code (made using the function "record"), but when I try to Run it on other images, it always give the the error of "there is no image open". I'm trying to fix this for a few days, but I couldn't yet, so I would appreciate a lot if you could give me some advice on this.


setMinAndMax(20, 86);
run("Apply LUT");
run("Close");
setAutoThreshold("Default");
//run("Threshold...");
setThreshold(0, 127);
setOption("BlackBackground", false);
run("Convert to Mask");
run("Close");
run("Fill Holes");
run("Watershed");
run("Analyze Particles...", "size=55-Infinity pixel circularity=0.70-1.00 show=Outlines display exclude clear add");


As I said, pretty simple code, only working on preparing the image and analyzing particles at the end.

Thanks in advance!

[Coolarj]

Hi everyone, thank you for all your questions, sorry I haven't been able to reply to them all. I haven't used ImageJ in some years, so unfortunately I can't answer many of your specific questions.

[katierussart]

Thanks for the video. Is there a way to do this same process with just part of the image? (A contour is drawn around the region of interest?)

[vetdrpradip]

I have question regarding macro writing ...I would like to have individual results of images processed displayed along with summary. Currently I can only get summary of particles from all images and last image results only.

[anishprasanna]

I followed all the instructions from the document, but I get a no images open error after I hit the process button. Any help would be appreciated.

[siddheshchavan]

If I have 1K TIFF images then how can I get the 3D CAD model from TIFF files ?

[aprilpeterson]

thanks for the video and macro code. I wish there were more video examples like this. Are you familiar with writing ImageJ macros in Java?

[moscovita]

thanks for the video.

I have 900 hypocotyls to measure, 10 in each foto. So your video is very usefull cause I can make it automatically.

The problem is that I need the proper macro that allows me to calculate the length between the root and the cotyledons, which could perhaps be determined by the colour (my hypocotyls are purple).

So, should I make my own macros? how would I do that?

[hammao]

Hi Arjun,

Thanks for the Video, can you please provide a different link for the Doc. I'm having problem downloading it from scribd.

[satyabratabarik]

can you please send the macro code you created ???

[lalithasivaraj]

Is it possible to get the macro code ?

[vladbio]

How can I use Macros or Batch processibg in JMicroVision.

somebody SOS ;(