3d segmentation unit vs pixels measures

[Василий Попков]

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?

--
Vasily A Popkov
Lab.Structure and function of mitochondria
A.N.Belozersky Institute of Physico-Chemical Biology
Moscow State University

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Thomas Boudier-4]

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

[Василий Попков]

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
>

--
Vasily A Popkov
Lab.Structure and function of mitochondria
A.N.Belozersky Institute of Physico-Chemical Biology
Moscow State University

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Thomas Boudier-4]

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.
/**************************************************************/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Priyanka Tomar]

How can we analyse four phases containing images using imagej
On Mar 3, 2016 3:04 PM, "Thomas Boudier" <[hidden email]> wrote:

> 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.
> /**************************************************************/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html