http://imagej.273.s1.nabble.com/Issues-with-analyze-particules-in-batch-mode-roi-became-black-tp5021305p5021306.html
> hello, it makes somes days that i try to run an particules analysis with
> thoses steps:
>
> //00 - define image directory
> //01 - rotates pictures with name finishing with"-07", “-08”, …, “-12”.
> //02 - show active picture
> //03 - create 3 “roy” .
> //04 - Combine Roys
> //05 - delete outside of the combined roy
> //06 - select “paintbrush” tool
> //07 - define the treshold level
> //08 - Finalisation and validation by user of treshold settings
> //09 - make binary
> //10 - Convert picture in 8-bits.
> //11 - fill holes
> //12 - do an analyze of particules
> //13 - saves results
> //14 - close everything exept “Results” and “Log”
> //15 - delete roys for the next picture
>
> I got several issues:
>
> FOR “//12 - do an analyze of particules” : if i choose Outlines or Masks
> results are the same.
>
> my program has worked for 26 pictures and now the second square become all
> black whatever the treshold level defined (attached picture).
>
> -the results excel built is in xls and a message appears when i open it, the
> message says that the format and the extension of the document is dose’nt
> match.
>
> This is the program i built:
>
> //00 - define image directory
> dir = getDirectory(“image”); //define dir for saving names
> name = getTitle; //define the name of the picture for savings
> index = lastIndexOf(name, “.”); //define index for savings
>
> //01 - rotates pictures with name finishing with"-07", "-08", ..., "-12".
> list2=substring(name, 0, (lengthOf(name)-4)); //cut the end of the picture
> name
> if (endsWith(list2, “-07”)) //if the end of the picture name is “-07”
> run("Rotate… “, “angle=180 interpolation=None”); // do a rotation of 180°
> if (endsWith(list2, “-08”)) //if the end of the picture name is -08”
> run("Rotate… ", “angle=180 interpolation=None”); // do a rotation of 180°
> if (endsWith(list2, “-09”)) //if the end of the picture name is “-09”
> run("Rotate… ", “angle=180 interpolation=None”); // do a rotation of 180°
> if (endsWith(list2, “-10”)) //if the end of the picture name is “-10”
> run("Rotate… ", “angle=180 interpolation=None”); // do a rotation of 180°
> if (endsWith(list2, “-11”)) //if the end of the picture name is “-11”
> run("Rotate… ", “angle=180 interpolation=None”); // do a rotation of 180°
> if (endsWith(list2, “-12”)) //if the end of the picture name is “-12”
> run("Rotate… ", “angle=180 interpolation=None”); // do a rotation of 180°
>
> //02 - show active picture
> setBatchMode(false); //show active picture
>
> //03 - create 3 "roy" .
> run(“ROI Manager…”); //lauch of roy manager
> makeRectangle(504, 204, 215, 381); // define the first square
> roiManager(“add”); // add first square to roi
> makeRectangle(262, 204, 224, 362); // define the second square
> roiManager(“add”); // add second square to roi
> makeRectangle(537, 630, 149, 116); // define the third square
> roiManager(“add”); // add third square to roi
> roiManager(“select”, newArray(0,1,2)); // select all roys
>
> //04 - Combine Roys
> roiManager(“Combine”); // combine all roys
> roiManager(“add”); // add to roy manager the combined roy
> roiManager(“select”, 3); // select the combined roy
>
> //05 - delete outside of the combined roy
> run(“Clear Outside”); // clear outside the combined roy
>
> //06 - select "paintbrush" tool
> setTool( “Paintbrush Tool” ); // select “paintbrush” tool
>
> //07 - define the treshold level
> setThreshold(185, 255); // define the treshold level
> run(“Threshold…”); // run threshold
>
> //08 - Finalisation and validation by user of treshold settings
> waitForUser(“définir le threshold et appuyer sur OK”); //wait user for
> clicing to “ok”
>
> //09 - make binary
> run(“Make Binary”); //make binary
>
> //10 - Convert picture in 8-bits.
> run(“8-bit”); //Convert picture in 8-bits.
>
> //11 - fill holes
> run(“Fill Holes”); // fill holes
>
> //12 - do an analyze particules
> run(“Analyze Particles…”, “size=50-Infinity show=Outlines display exclude
> include summarize”);
>
> //13 - saves results
> selectWindow(“Results”); // select “results windows”
> getResult (“Area”, 0); // selectionne “Area column”
> if (index!=-1) name = substring(name, 0, index); // too smart for me
> name = name + “.xls”; // transform name for creating excel file
> saveAs(“Results…”, dir+name); //saves results (step 1)
> print(dir+name); //saves result (step 2)
>
> //14 - close everything exept "Results" and "Log"
> close();
> //15 - delete roys for the next picture
> roiManager(“Deselect”); //select all roys
> roiManager(“Delete”); //delete all roys
>
> I’m not a programmer, i founded parts of code on internet and on this forum
> in order to create this program
>
> If someone can help me, thank you A LOT. :slight_smile:
>
> <
http://imagej.1557.x6.nabble.com/file/t382132/SO%2BGL-00007-01-05.jpg>
>
>
>
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