http://imagej.273.s1.nabble.com/HyperStack-guidance-Java-plugin-API-tp5024450p5024453.html
> On Feb 11, 2021, at 15:46, Fred Damen <
[hidden email]> wrote:
>
> Greetings Kenneth,
>
> This is most of what I do in ImageJ; Process MRI datasets where volumes
> are acquired under a series of slightly different circumstances and then
> extract information therefrom.
>
> Check out
https://imagej.net/Frames>
> F_Profile is nice for looking at your raw data in the frame(time not RGB)
> direction.
> F_Project is used to process data in the frame direction. The GUI is
> useful for the quick and dirty, but what your looking for is the Compute
> interface and compute method; fully threaded...
> If your frames vary other than by index you will want to add slice labels
> to each frame(first slice).
> F_Slider is useful to viewing the varied output of processing the frame data.
>
>
> Enjoy,
>
> Fred
>
> PS. Anyone know when imagej.net will be writable again?
>
>
> On Thu, February 11, 2021 12:43 pm, Kenneth Sloan wrote:
>> Many of my plugins deal with volume data (approximately 1500x750x100 -
>> 1500x750 images, 100 slices).
>> For those for whom it might matter - these are OCT images of human retina.
>>
>> I now need to process time sequences, (xyz)t - I estimate 2-50 time
>> points. (these would be several imaging sessions ("visits")). The
>> subsequent visits are (claimed to be) registered with the first visit.
>> If it turns out they are not...I can deal with that.
>>
>> The images are all single channel grayscale images (32-bit floats) - but
>> this is negotiable. In particular, I could probably make do with 8-bit
>> samples.
>>
>> My question is: is this a good fit for the ImageJ HyperStack mechanism?
>> My only doubts come from the frequent phrase "must be RGB" I have seen
>> while superficially browsing the documentation. This may be because the
>> documentation appears to refer to specific interactive tools, where
>> multiple channels appear to be very important.
>>
>> I'm primarily interested in programatic manipulation in Java plugins.
>>
>> Going further...my current usage involves a Extension to StackWindow (and
>> ImagePlus) to link a displayed volume with yet another stack of images
>> (not a "volume" - just a stack of related images - these are all "en face"
>> images). So, I anticipate that I might want to make similar extensions to
>> deal with a displayed HyperStack. This is desirable - but probably not
>> essential, if it matters.
>> Actually, I can see a case for making *that* stack into a HyperStack -
>> again adding a "visit" time parameter.
>>
>> I would appreciate guidance on what parts of the ImageJ API I should pay
>> attention to. Where should I start? I suppose I'm hoping for something
>> analogous to a StackWindow API ("HyperStackWindow"?).
>>
>> Examples of Java code dealing with a similar situation ((xyz)t images - no
>> "channels") would be pure gold.
>>
>> --
>> Kenneth Sloan
>>
[hidden email]
>> Vision is the art of seeing what is invisible to others.
>>
>> --
>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
>
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