Extraction of slice having the maximum intensity in a specific channel

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Extraction of slice having the maximum intensity in a specific channel

cbenji59
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! :)



Results windows of measurment from the macro
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Re: Extraction of slice having the maximum intensity in a specific channel

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



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

gankaku
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.
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>
>>
>>
>> --
>>
>> CEO: Dr. rer. nat. Jan Brocher
>> phone:  +49 (0)6234 917 03 39
>> mobile: +49 (0)176 705 746 81
>> e-mail: [hidden email]
>> info: [hidden email]
>> inquiries: [hidden email]
>> web: www.biovoxxel.de
>>
>

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

cbenji59
Great! Many thanks for this link, I didn't find it out.
I made few modification for extracting the channels referring to the same slice, and it works perfectly!

Many thanks for your help! :)