iterating over slices in volume?

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iterating over slices in volume?

Kenneth Sloan-3
I apologize if this is a repeat - I didn’t see it post and I haven’t seen a reply.  I think this is easy.

I need to iterate a process over all slices of a volume (the current candidate is to adjust Brightness&Contrast.  Can someone please provide a pointer on how to do this?

In processing these volumes, I first handle individual slices as individual images - but they are then aligned and cropped and assembled into a volume.  The cropping changes enough things so that another pass of adjusting brightness & contrast is called for.  I’d like to avoid unpacking the volume into a collection of separate files, using Batch Processor to adjust them, and then re-assemble.  Is there a way to iterate through the slices “in place”?


Kenneth Sloan
[hidden email]




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Re: iterating over slices in volume?

Herbie
Good day Kenneth,

a simple answer is, by looping over all slices of the volume and using
the macro function

        setSlice( i );

"Displays the i-th slice of the active stack. Does nothing if the active
image is not a stack."

But I fear you're looking for something different -- no?

Best

Herbie

:::::::::::::::::::::::::::::::::::::::::::
Am 15.03.17 um 16:14 schrieb Kenneth Sloan:

> I apologize if this is a repeat - I didn’t see it post and I haven’t
> seen a reply.  I think this is easy.
>
> I need to iterate a process over all slices of a volume (the current
> candidate is to adjust Brightness&Contrast.  Can someone please
> provide a pointer on how to do this?
>
> In processing these volumes, I first handle individual slices as
> individual images - but they are then aligned and cropped and
> assembled into a volume.  The cropping changes enough things so that
> another pass of adjusting brightness & contrast is called for.  I’d
> like to avoid unpacking the volume into a collection of separate
> files, using Batch Processor to adjust them, and then re-assemble.
> Is there a way to iterate through the slices “in place”?
>
> — Kenneth Sloan [hidden email]
>
>
>
>
> -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: iterating over slices in volume?

ctrueden
In reply to this post by Kenneth Sloan-3
Hi Kenneth,

> I apologize if this is a repeat - I didn’t see it post and I haven’t
> seen a reply.

You can search the ImageJ list archives by visiting
https://search.imagej.net/, typing the subject of your last post in quotes
(which was "adjust B&C o every slice of a volume"), and then clicking the
big green "ImageJ" button in the "Forum + Lists" section. Then you will see
that your previous mail did indeed post, and you even got a reply from
Michael Schmid:

http://imagej.1557.x6.nabble.com/adjust-B-amp-C-o-every-slice-of-a-volume-tt5018289.html#a5018300

Regards,
Curtis


--
Curtis Rueden
LOCI software architect - https://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Wed, Mar 15, 2017 at 10:14 AM, Kenneth Sloan <[hidden email]>
wrote:

> I apologize if this is a repeat - I didn’t see it post and I haven’t seen
> a reply.  I think this is easy.
>
> I need to iterate a process over all slices of a volume (the current
> candidate is to adjust Brightness&Contrast.  Can someone please provide a
> pointer on how to do this?
>
> In processing these volumes, I first handle individual slices as
> individual images - but they are then aligned and cropped and assembled
> into a volume.  The cropping changes enough things so that another pass of
> adjusting brightness & contrast is called for.  I’d like to avoid unpacking
> the volume into a collection of separate files, using Batch Processor to
> adjust them, and then re-assemble.  Is there a way to iterate through the
> slices “in place”?
>
> —
> Kenneth Sloan
> [hidden email]
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
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Re: iterating over slices in volume?

Kenneth Sloan-3
Thanks - I missed the reply.

> On Mar 15, 2017, at 10:47, Curtis Rueden <[hidden email]> wrote:
>
> Hi Kenneth,
>
>> I apologize if this is a repeat - I didn’t see it post and I haven’t
>> seen a reply.
>
> You can search the ImageJ list archives by visiting
> https://search.imagej.net/, typing the subject of your last post in quotes
> (which was "adjust B&C o every slice of a volume"), and then clicking the
> big green "ImageJ" button in the "Forum + Lists" section. Then you will see
> that your previous mail did indeed post, and you even got a reply from
> Michael Schmid:
>
> http://imagej.1557.x6.nabble.com/adjust-B-amp-C-o-every-slice-of-a-volume-tt5018289.html#a5018300
>
> Regards,
> Curtis
>
>
> --
> Curtis Rueden
> LOCI software architect - https://loci.wisc.edu/software
> ImageJ2 lead, Fiji maintainer - https://imagej.net/User:Rueden
> Did you know ImageJ has a forum? http://forum.imagej.net/
>
>
> On Wed, Mar 15, 2017 at 10:14 AM, Kenneth Sloan <[hidden email]>
> wrote:
>
>> I apologize if this is a repeat - I didn’t see it post and I haven’t seen
>> a reply.  I think this is easy.
>>
>> I need to iterate a process over all slices of a volume (the current
>> candidate is to adjust Brightness&Contrast.  Can someone please provide a
>> pointer on how to do this?
>>
>> In processing these volumes, I first handle individual slices as
>> individual images - but they are then aligned and cropped and assembled
>> into a volume.  The cropping changes enough things so that another pass of
>> adjusting brightness & contrast is called for.  I’d like to avoid unpacking
>> the volume into a collection of separate files, using Batch Processor to
>> adjust them, and then re-assemble.  Is there a way to iterate through the
>> slices “in place”?
>>
>> —
>> Kenneth Sloan
>> [hidden email]
>>
>>
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html


Kenneth Sloan
[hidden email]




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