I am trying to measure area% using FIJI particle analysis, but i cannot figure out how to build a macro

Hello Stackoverflow users,

I am currently working on my bachelors thesis, and i have over 1.000 images to analyze. For this reason, i would like to make a macro that can crop these images the same way, apply the same color threshold and measure area% above this threshold; and then adding them into one csv/excel/text file.Example of the Winogradsky column, containing the sulfur reducing bacteria i would like to analyze.I added an example image, and i would like to analyze what % of this image is black.

I have tried to manually crop the images, add the correct colour filter, then do a particle analysis. however every time i do this, i get absurdly low area%, trying to put this into a macro as shown below also does not work. I have added the macro i tried to make below, as you can probably see; i am quite new to image analysis.

//seting directory
input=getDirectory("Set directory here");
list = getFileList(input);
for (i = 0; i < list.length; i++)
        Wholecolor(input, list[i]);
function Wholecolor (input,filename){
    open (input + filename);

//open ROI manager
run("ROI Manager...");
roiManager("Show All");

// Assign raw opened image the name "currentImage"
currentImage=getImageID();

// cropping image
makeRectangle(834, 414, 3840, 3468);
run("Crop");

//Duplicate raw image to make a copy that will be modified to make a mask
run("Duplicate...", "title=Mask");

// Highlight the "Mask" image as the duplicate that will be thresholded to make the mask
selectWindow("Mask");
makeRectangle(1026, 492, 3504, 3294);
setBackgroundColor(0, 0, 0);
run("Clear Outside");
run("Color Threshold...");

// Color Thresholder 2.14.0/1.54f
// 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]=30;
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 Thresholding-------------

run("Analyze Particles...", "display exclude clear summarize overlay");
    // Get particle analysis results and put them into a file 

//clear ROI manager and Mask image so there is a clean workspace for the next image in the folder
roiManager("Deselect");
roiManager("Delete");
close("Mask");
close(filename+"_HSB");

//save data collected by ROI manager to a .csv file titled "WInogradksy_results"

   dir=getDirectory("image");
   //Change the file name here
   name = "Winogradsky_results"; 
   index = lastIndexOf(name, "\\"); 
   if (index!=-1) name = substring(name, 0, index); 
   name = name + ".csv"; ///can change xls to csv, txt, etc.
   saveAs("Measurements", dir+name); 
   
close();
}
run("Clear Results");

I would appreciate any help with this problem, many thanks in advance!

i would like to analyze what % of this image is black.

The first thing to do is: Define "black" (in your context).

Below please find what I get by applying the "Default"-threshold scheme to the "Hue"-channel of your sample image.

The corresponding %Area is about 27.22%.

The following ImageJ-macro code may get you started:

run("Set Measurements...","area area_fraction display redirect=None decimal=2");
run("HSB Stack");
setAutoThreshold("Default dark");
run("Measure");