Re: Extraction of slice having the maximum intensity in a specific channel

Posted by gankaku on Aug 01, 2016; 11:04am
URL: http://imagej.273.s1.nabble.com/Extraction-of-slice-having-the-maximum-intensity-in-a-specific-channel-tp5016959p5016963.html

Sorry, link missing. So, here we go:
http://forum.imagej.net/t/maximum-intensity-z-project-alters-values-randomly/2193/2

Am 01.08.2016 13:09 schrieb "BioVoxxel" <[hidden email]>:

> Sorry, link missing. So, here we go:
>
> http://forum.imagej.net/t/maximum-intensity-z-project-alters-values-randomly/2193/2
>
> Am 01.08.2016 12:12 schrieb "BioVoxxel" <[hidden email]>:
>
>> Hi cbenji59,
>>
>> the following ImageJ forum post might help you in achieving your goal.
>> The macro, presented there basically measures the intensity and extracts
>> the respective brightest slice from a xyzt-stack.
>> You can accordingly adjust this to make it work for your type of stacks.
>>
>> kind regards,
>> Jan
>>
>> 2016-08-01 9:38 GMT+02:00 cbenji59 <[hidden email]>:
>>
>>> Dear,
>>>
>>> I am struggling with making a plugging in ImageJ / FiJi.
>>> What I want to do, is from a TIFF file from a 13 stacks in Z, several
>>> point
>>> in time, and 4 channels, to create a new file (extraction) from the slice
>>> where there is more intensity.
>>> Indeed, during my acquisition, I made a Z stack, I am only interested on
>>> having one slice, which is the more intense in the fluorescent channel.
>>>
>>> Up-to-there, I am able to measure intensity in all the channel, all the
>>> time, and all the slice, but unable to from that to extract data in a way
>>> that I can ask the following:
>>>
>>> "for each slice, which slice present the highest value in intensity"
>>>
>>> Indeed, from that, I would be able to extract the given slice (for the 4
>>> channels) and make a new file containing only the brightest slice for
>>> each
>>> time, based only on the value of the fluorescent channel (here channel 4
>>> on
>>> the figure below).
>>>
>>> Would it be possible to help me on this macro or maybe some have idea
>>> about
>>> an easiest way?
>>> Many thanks by advance! :)
>>>
>>>
>>>
>>> <http://imagej.1557.x6.nabble.com/file/n5016959/results.png>
>>>
>>>
>>>
>>> --
>>> View this message in context:
>>> http://imagej.1557.x6.nabble.com/Extraction-of-slice-having-the-maximum-intensity-in-a-specific-channel-tp5016959.html
>>> Sent from the ImageJ mailing list archive at Nabble.com.
>>>
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>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>
>>
>>
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>>
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>

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