Posted by
Thomas Boudier-4 on
URL: http://imagej.273.s1.nabble.com/3d-segmentation-unit-vs-pixels-measures-tp5015529p5015778.html
Hi Vasily,
You can see voxels as cubes in the image space, so if you want to
compute volumes in um^3, you count the number of voxels and multiply by
the volume as one voxel as you mentioned. So in the case 2 you may find
bigger volumes in um^3 with less voxels, because voxels in 2 are bigger
that in 1. Hope this helps.
Best,
Thomas
On 29/02/2016 20:30, Василий Попков wrote:
> Hello.
> I have the same problem for spot segmentation. pixel volume = unit volume.
> Is there any way to understand what "the real" volume is, from pixel one?
> Or to compare to images.
>
> For example if I have 2 objects on different images with 100 pixel volume
> and raw images are
> 7 pixels per µm
> 1) Voxel size: 0.1428x0.1428x0.25 µm^3
> 2) Voxel size: 0.1428x0.1428x0.3158 µm^3
>
> Can I count it somehow? Since voxels are not cubical I am a bit confosed.
>
> I guess I can say that V(1)/V(2) = (0.25)/(0.31) am I right?
> Can I say, that theirs volume = v(pixel)*0.14*0.14*0.3185 or
> v(pixel)*0.14*0.14*0.25?
>
> Thank you for clarifying it.
>
> 2016-02-11 10:39 GMT+03:00 Thomas Boudier <
[hidden email]>:
>
>> Hi,
>>
>> The "simple segmentation" plugin does not copy the calibration properties
>> from the raw image to the segmented image, this bug will be fixed in a next
>> update.
>>
>> Best,
>>
>> Thomas
>>
>>
>> On 03/02/2016 20:07, Василий Попков wrote:
>>
>>> Good time of a day. I am using 3d segmentation package (
>>>
http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_ij_suite:start).
>>> And I have exactly the same values for pixels volumes and unity volumes
>>> for
>>> each image (in output), which is obviously not true. There is information
>>> about voxel size in image info, but it seems it is not used.
>>>
>>> Anyone can give me a tip how I can make it to give me correct values in
>>> mkm?
>>>
>>>
>> --
>> /***************************************************************/
>> Thomas Boudier, Associate Professor, UPMC,
>> Université Pierre et Marie Curie, Paris, France.
>> BioInformatics Institute (BII)/IPAL, Singapore.
>> /**************************************************************/
>>
>> --
>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
>
>
--
/***************************************************************/
Thomas Boudier, Associate Professor, UPMC,
Université Pierre et Marie Curie, Paris, France.
BioInformatics Institute (BII)/IPAL, Singapore.
/**************************************************************/
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