> On Feb 1, 2016, at 13:28, Saalfeld, Stephan <
[hidden email]> wrote:
>
> Hi Kenneth,
>
> the Calibration object has a pixelDepth field.
>
> For non-homegeneous z-spacing, I suggest to use TrakEM2 where this is
> possible and the norm. It also has a built in mechanism to calculate
> this spacing from aligned serial section image data
>
>
http://fiji.sc/Fiji/Z-Spacing_Correction <
http://fiji.sc/Fiji/Z-Spacing_Correction>
>
> based on this paper
>
>
http://arxiv.org/pdf/1411.6970v2.pdf <
http://arxiv.org/pdf/1411.6970v2.pdf>
>
> Best,
> Stephan
>
>
>
> On Mon, 2016-02-01 at 13:13 -0600, Kenneth Sloan wrote:
>> Please excuse me for piggy-backing on this discussion, but…
>>
>> With the rise in Stack processing - are there similar mechanisms to record, remember, and report back on the depth of voxels? Simplest would be “getVoxelSize(unit, voxelWidth, voxelHeight, voxelDepth)” - but…I’ll take what I can get.
>>
>> Pressing my luck - it’s common for slices in a stack to be less regularly spaced than, say, rows in an image. Is there any mechanism for mapping slice number -> z value?
>>
>> —
>> Kenneth Sloan
>>
[hidden email] <mailto:
[hidden email]> <mailto:
[hidden email] <mailto:
[hidden email]>>
>> Vision is the art of seeing what is invisible to others.
>>
>>> On Feb 1, 2016, at 07:45, BenDehap <
[hidden email]> wrote:
>>>
>>> Hello Michael,
>>>
>>> First thank you for your answer, someone give me a simple way to resolve my
>>> problem as following :
>>>
>>>
>>> getPixelSize (unit, pixelWidth, pixelHeight);
>>> if (unit=="microns"){
>>> x=pixelWidth;}
>>> else exit ("No calibration");
>>>
>>> but i seen that the method you propose is widely used on forums.
>>> Would it be possible to show me an example of code using "x" for the value
>>> of the pixel witdh and "image1" for the name of my image.
>>>
>>> I don't know if you have the time to do it, but i'm a coding beginner and i
>>> feell a bit lost.
>>>
>>> Thanks anyway.
>>>
>>> Ben
>>>
>>>
>>> 2016-02-01 11:15 GMT+01:00 Michael Entrup [via ImageJ] <
>>>
[hidden email]>:
>>>
>>>> Hi Ben,
>>>>
>>>> each ImagePlus [1] has a method called ``getCalibration()``. It returns
>>>> the Calibration [2] instance of the ImagePlus. The Calibration Object
>>>> contains all the methods you need. ``getUnit()`` returns a String to
>>>> check if the unit is µm. ``getX(double x)`` converts a pixel value into
>>>> a physical unit.
>>>>
>>>> Best regards
>>>> Michael
>>>>
>>>> [1]:
http://rsb.info.nih.gov/ij/developer/api/ij/ImagePlus.html>>>> [2]:
http://rsb.info.nih.gov/ij/developer/api/ij/measure/Calibration.html>>>>
>>>>
>>>> On 31.01.2016 20:37, BenDehap wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> I have a simple problem and reading different forums didn't help me to
>>>>> resolve it.
>>>>>
>>>>> I need for my ImageJ Plugins to attribute to a variable "x" the value of
>>>> the
>>>>> pixel size in "µm" used in my pre-calibrated "image1".
>>>>>
>>>>> It would really help me if someone can help me on this case.
>>>>>
>>>>> Thanks very much.
>>>>>
>>>>> Ben
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> View this message in context:
>>>>
http://imagej.1557.x6.nabble.com/Get-the-pixel-Size-tp5015501.html>>>>> Sent from the ImageJ mailing list archive at Nabble.com.
>>>>>
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http://imagej.nih.gov/ij/list.html>>>>>
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