Re: distance measurement and cropping behavior questions

Posted by Cammer, Michael on
URL: http://imagej.273.s1.nabble.com/distance-measurement-and-cropping-behavior-questions-tp5020756p5020765.html

The screenshot at the left shows the correct measurement on the original image.  (If not attached, see https://www.flickr.com/photos/mcammer/42499032731/ ) The screenshot at the right shows a line profile plot where the first measurement of the line segment is 1.05 um.  Then I dragged the endpoint a pixel or two and measured again and got what appears to be a correct 0.62 um.
Not shown, dragging it a few pixels again went to 1.82, 2.62, 8.55 um.   The length numbers in the status bar jump around and go to the results window if measured.
Also, the angle is reported wrong.

Thank you!

Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory
NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY  10016
[hidden email]  http://nyulmc.org/micros  http://microscopynotes.com/ 
Voice direct only, no text or messages:  1-914-309-3270 and 1-646-501-0567



-----Original Message-----
From: Michael Schmid [mailto:[hidden email]]
Sent: Friday, June 1, 2018 4:56 AM
To: [hidden email]
Subject: Re: distance measurement and cropping behavior questions

Hi Michael,

(1) Plot profile: Yes, the x axis is calibrated length.
There is a small difference between the length reported by "measure" and
the length of the line section of a profile plot (corresponding to less
than one pixel):
Profile plots sample the image with a spacing of one pixel. If the
length of the line is not an integer number of pixels, the length of the
profile will still be an integer number of pixels (apart from rounding
errors).

Is it this (small) differences of profile lengths and actual line
lengths (given by 'measure') that you refer to?

If not, it would be good to have a sample image and test macro to trace
down the reason for the problem.


(2) Crop using the wrong place: Using Linux and Java 1.8, I have never
seen that (I'm working mostly with 32-bit images). Again a sample image
and test macro would help.


Michael
________________________________________________________________
On 31/05/2018 19:09, Cammer, Michael wrote:

> I was wondering whether anybody else is having odd behaviors with ImageJ  1.52d8 with Java 1.8 on Windows 7?  One of them may be my fault and want to confirm; the other is something odd with the software.
>
> 1.
> When I do a line profile plot and measure a distance on it, most of the time the distance returned is incorrect.
> I thought that when the images were spatially calibrated, the plot also was supposed to return the calibrated length.  Am I mistaken about this or is this a bug?  What makes me puzzled is that the lengths reported are inconsistent.
>
> 2.
> When I draw a rectangle on an image and then crop, the upper left of the image is cropped instead of the ROI.  The resultant image is the size of the ROI, but not the correct location.
> When I duplicate, the correct region is duplicated.
> These are 4096 x 4096 pixels 16 bit and 32bit images generated with a Talos TEM and Gatan camera.  When the images are converted to RGB or 8 bit, this problem does not happen.
>
> Any help appreciated.
>
> Thank you.
>
> Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory
> NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY  10016
> [hidden email]<mailto:[hidden email]>  https://urldefense.proofpoint.com/v2/url?u=http-3A__nyulmc.org_micros&d=DwICaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=IQJBKDQyf9pJJ2Xyr7E8_unF-qqJFrkq6n56m94c6Yg&s=A4IYO_4gSzK-x6uW7AZHCcvBYyFdSw-9OmxQTTzKtuE&e=  https://urldefense.proofpoint.com/v2/url?u=http-3A__microscopynotes.com_&d=DwICaQ&c=j5oPpO0eBH1iio48DtsedbOBGmuw5jHLjgvtN2r4ehE&r=oU_05LztNstAydlbm5L5GDu_vAdjXk3frDLx_CqKkuo&m=IQJBKDQyf9pJJ2Xyr7E8_unF-qqJFrkq6n56m94c6Yg&s=rEsI6lG7KEwjD5s5vWnD6XRstmahy5rONbvMS7FfHag&e=
> Voice direct only, no text or messages:  1-914-309-3270 and 1-646-501-0567
>

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