This macro happily rotates the individual selections and makes them into a
montage.
Note I reduced the image to 8 bit to simplify thresholding, but the method
works on RGB images
run("8-bit");
setAutoThreshold("Huang dark no-reset");
run("Create Selection");
run("Fill", "slice");
run("Select None");
setThreshold(0,254);
UseImageID=getImageID();
roiManager("reset");
run("Analyze Particles...", "size=200-Infinity add");
//resetThreshold;
Nrois=roiManager("count");
for (i = 0; i <= Nrois-1; i++) {
selectImage(UseImageID);
roiManager("select", i);
run("Fit Rectangle");
run("Duplicate...", " ");
rename("blob"+i);
}
run("Images to Stack", " title=blob fill=#ffffff use keep");
run("Make Montage...", "columns=1 rows=Nrois scale=1 border=4 use");
Jeremy
===============================================
B i o V i s P l a t f o r m of Uppsala University
Light & EM microscopy / FlowCytometry & Cell Sorting / Image
Analysis
===============================================
Jeremy Adler PhD - Senior research engineer
Light, Confocal Microscopy, Image Analysis
E-mail: [email protected]
0739 188170
www.uu.se/biovis
Dag Hammarskjölds v 20
751 85 UPPSALA, SWEDEN
http://biovis.uu.se/
===============================================
-----Original Message-----
From: Herbie <[email protected]>
Sent: Thursday, January 23, 2025 4:19 PM
To: [email protected]
Subject: Re: can't rotate pasted image
Thanks Kees,
this was of course a typo in my mail.
It doesn't change the problem!
Thanks
Herbie
:::::::::::::::::::::::::::::::::::::::::::::::::::
Am 23.01.25 um 14:56 schrieb Straatman, Kees (Dr.):
> Hi Herbie,
>
> It should be:
>
> run("Images to Stack","name=Seeds title=#");
> setBatchMode(false);
> exit();
>
> Best wishes
> Kees
>
> Advanced Imaging Facility (RRID: SCR_020967) University of Leicester
> http://www.le.ac.uk/advanced-imaging-facility
>
>
> -----Original Message-----
>
> Sent: 23 January 2025 12:56
> Subject: Re: can't rotate pasted image
>
> ***CAUTION:*** This email was sent from an EXTERNAL source. Think before
> clicking links or opening attachments.
>
> Dear Jeremy,
> dear listers!
>
> Attached please find my macro with the mechanism suggested by Jeremy!
>
> Interestingly, I wasn't able to make it work properly with
>
> run("Images to Stack","name=Seeds title=#");
> setBatchMode(true);
> exit();
>
> instead of
>
> setBatchMode("exit and display");
> run("Images to Stack","name=Seeds title=#");
> exit();
>
> In the former case, all slices are magically doubled.
>
> Regards
>
> Herbie
>
> :::::::::::::::::::::::::::::::::::::::::
> Am 22.01.25 um 18:32 schrieb Jeremy Adler:
>> A slightly simpler variant on Herbie's macro.
>>
>> Once you have a selection for single objects, use "Fit Rectangle" and then
>> duplicate.
>> The duplicated part of the image is rotated.
>>
>> Jeremy
>> ===============================================
>> B i o V i s P l a t f o r m of Uppsala University
>> Light & EM microscopy / FlowCytometry & Cell
>> Sorting / Image Analysis ===============================================
>> Jeremy Adler PhD - Senior research engineer
>> Light, Confocal Microscopy, Image Analysis
>> E-mail: [email protected]
>> 0739 188170
>> http://www.u/
>> u.se%2Fbiovis&data=05%7C02%7Ckrs5%40leicester.ac.uk%7C7d25261c29dc48b
>> 1
>> 8c2808dd3bb43805%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C0%7C6387323
>> 6
>> 7428985559%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLj
>> A
>> uMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7
>> C
>> &sdata=MTWYJHWhjuVbAAOMqDOry6BILoCUiFF8UshMPKyge7o%3D&reserved=0
>>
>> Dag Hammarskj lds v 20
>> 751 85 UPPSALA, SWEDEN
>> http://biovi/
>> s.uu.se%2F&data=05%7C02%7Ckrs5%40leicester.ac.uk%7C7d25261c29dc48b18c
>> 2
>> 808dd3bb43805%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C0%7C6387323674
>> 2
>> 9002201%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuM
>> D
>> AwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&s
>> d
>> ata=VtIDLjWUxSP3ejVIlph0DKyAPvKIj471O3akzrmiKTk%3D&reserved=0
>> ===============================================
>>
>>
>>
>>
>> -----Original Message-----
>> From: Herbie <[email protected]>
>> Sent: Wednesday, January 22, 2025 3:57 PM
>> To: [email protected]
>> Subject: Re: can't rotate pasted image
>>
>> Slightly off-topic William!
>>
>> Some years ago I was asked to write a macro that performs this task on rice
>> seeds.
>>
>> Attached please find the "revived" macro-code and a test-image.
>> The macro requires two ImageJ-plugins.
>>
>> Good to hear you resolved the Java-problem.
>>
>> Regards
>>
>> Herbie
>>
>> :::::::::::::::::::::::::::::::::::::::::
>> Am 22.01.25 um 13:04 schrieb William Rust:
>>> I'm writing code in java. What I am trying to do is take an image
>>> with
>>> 20 wheat kernels in a petri dish and put each kernel in its own
>>> image with the kernel rotated so all kernels are roughly vertical.
>>> Here's the code snippet where I am doing it.
>>>
>>> ImageProcessor newIp = new ColorProcessor(300, 300);
>>> ImagePlus newImp = new ImagePlus("sub " + idx, newIp);
>>> newIp.setColor(background);
>>> newIp.fill();
>>> imp.copy();
>>> newImp.paste();
>>> newImp.getProcessor().rotate(angle[idx]);
>>> newImp.updateAndDraw();
>>> newImp.show();
>>>
>>>
>>> Previously, I've cut the subimage out of the original image using
>>> the bounding box from analyze particles. The weirdness occurs
>>> somewhere between the paste and the rotate. The pasting works whether I do
>>> the rotate or not.
>>> But when I paste, the rotate does not work. And, if I don't paste,
>>> the rotate does work (I can tell this because the background is
>>> tilted after a rotate with no paste but not with rotate and paste).
>>> This snippet shows one of the things that I've tried, the updateAndDraw(),
>>> but nothing has worked.
>>> Any ideas on what I'm doing wrong?
>>>
>>> Thanks,
>>>
>>> wjr.
>>
>>
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