Stack control for turning individual slices on and off?

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Stack control for turning individual slices on and off?

Andy Schofield
Hi All,

I have a multiband, 16-bit per band satellite Tiff image and wondered if there are any tools/plugins available in Fiji that enables easy control over switching slices on and off so I can assess the alignment between the different bands (such as the layer control tool in Photoshop etc. for instance)?

Regards
Andy

BTW, in s similar vein, is there a tool/plugin that can manage the selective manual reordering of slices in a stack? I looked at the Image->Stacks->Tools->Stack Sorter but this seemed to be add/remove/duplicate or reverse/order by label only. I ended up renaming each slice to use th reorder by label but wondered if there was plugin that allows the idea of 'Move current slice to slice 6' for instance?


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Re: Stack control for turning individual slices on and off?

Christian Goosmann-2
Hi Andy
it sounds like you want to load your multiband image as a composite
stack in Fiji. If it doesn't automatically import as composite stack,
you have to import the single band (or channel) images as a simple stack
and use the 'Image>Hyperstacks>Stack to Hyperstack...' command. You end
up with a window with a slider to go through the channels. Open the
'channels tool' by hitting ctl+alt "z". Then you can set the upper
dropdown item in the tool to 'Composite' view. This shows you an overlay
of the channels and you can uncheck the ones you don't want to include.
You can pick different color luts for the individual channels, the
hyperstack is colorcoded in a default manner at the beginning.
Hth
Christian

---
Christian Goosmann
Mikroskopie
Max-Planck-Institut für Infektionsbiologie
Campus Charité Mitte
Charitéplatz 1
10117 Berlin
Tel.: +49 30 28460 388

Andy Schofield wrote:

> Hi All,
>
> I have a multiband, 16-bit per band satellite Tiff image and wondered if there are any tools/plugins available in Fiji that enables easy control over switching slices on and off so I can assess the alignment between the different bands (such as the layer control tool in Photoshop etc. for instance)?
>
> Regards
> Andy
>
> BTW, in s similar vein, is there a tool/plugin that can manage the selective manual reordering of slices in a stack? I looked at the Image->Stacks->Tools->Stack Sorter but this seemed to be add/remove/duplicate or reverse/order by label only. I ended up renaming each slice to use th reorder by label but wondered if there was plugin that allows the idea of 'Move current slice to slice 6' for instance?
>
>
> The information contained in this message is intended for the addressee only and may contain sensitive information. If you are not the addressee, please delete this message and notify the sender; you should not copy or distribute this message or disclose its contents to anyone. Any views or opinions expressed in this message are those of the individual(s) and not necessarily of the organisation. No reliance may be placed on this message without written confirmation from an authorised representative of its contents. No guarantee is implied that this message or any attachment is virus free or has not been intercepted and amended.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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Correction: Re: Stack control for turning individual slices on and off?

Christian Goosmann-2
Sorry, Ctl+Shift "Z" opens the channels tool of course.
C.

---
Christian Goosmann
Mikroskopie
Max-Planck-Institut für Infektionsbiologie
Campus Charité Mitte
Charitéplatz 1
10117 Berlin
Tel.: +49 30 28460 388

Christian Goosmann wrote:

> Hi Andy
> it sounds like you want to load your multiband image as a composite
> stack in Fiji. If it doesn't automatically import as composite stack,
> you have to import the single band (or channel) images as a simple
> stack and use the 'Image>Hyperstacks>Stack to Hyperstack...' command.
> You end up with a window with a slider to go through the channels.
> Open the 'channels tool' by hitting ctl+alt "z". Then you can set the
> upper dropdown item in the tool to 'Composite' view. This shows you an
> overlay of the channels and you can uncheck the ones you don't want to
> include. You can pick different color luts for the individual
> channels, the hyperstack is colorcoded in a default manner at the
> beginning.
> Hth
> Christian
>
> ---
> Christian Goosmann
> Mikroskopie
> Max-Planck-Institut für Infektionsbiologie
> Campus Charité Mitte
> Charitéplatz 1
> 10117 Berlin
> Tel.: +49 30 28460 388
>
> Andy Schofield wrote:
>> Hi All,
>>
>> I have a multiband, 16-bit per band satellite Tiff image and wondered
>> if there are any tools/plugins available in Fiji that enables easy
>> control over switching slices on and off so I can assess the
>> alignment between the different bands (such as the layer control tool
>> in Photoshop etc. for instance)?
>>
>> Regards
>> Andy
>>
>> BTW, in s similar vein, is there a tool/plugin that can manage the
>> selective manual reordering of slices in a stack? I looked at the
>> Image->Stacks->Tools->Stack Sorter but this seemed to be
>> add/remove/duplicate or reverse/order by label only. I ended up
>> renaming each slice to use th reorder by label but wondered if there
>> was plugin that allows the idea of 'Move current slice to slice 6'
>> for instance?
>>
>>
>> The information contained in this message is intended for the
>> addressee only and may contain sensitive information. If you are not
>> the addressee, please delete this message and notify the sender; you
>> should not copy or distribute this message or disclose its contents
>> to anyone. Any views or opinions expressed in this message are those
>> of the individual(s) and not necessarily of the organisation. No
>> reliance may be placed on this message without written confirmation
>> from an authorised representative of its contents. No guarantee is
>> implied that this message or any attachment is virus free or has not
>> been intercepted and amended.
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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Re: Correction: Re: Stack control for turning individual slices on and off?

Andy Schofield
Thanks Christian.

That was just what I was after. Switching to the Grayscale view on the Channel Tools dialog box helped a lot too as that meant the channel check boxes were mutually exclusive, enabling the visual 'flicker' between two bands.

On the BTW addendum, any thoughts on that sort of slice control too?

Regards
Andy

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Christian Goosmann
Sent: 29 June 2017 12:34
To: [hidden email]
Subject: Correction: Re: Stack control for turning individual slices on and off?

Sorry, Ctl+Shift "Z" opens the channels tool of course.
C.

---
Christian Goosmann
Mikroskopie
Max-Planck-Institut für Infektionsbiologie Campus Charité Mitte Charitéplatz 1
10117 Berlin
Tel.: +49 30 28460 388

Christian Goosmann wrote:

> Hi Andy
> it sounds like you want to load your multiband image as a composite
> stack in Fiji. If it doesn't automatically import as composite stack,
> you have to import the single band (or channel) images as a simple
> stack and use the 'Image>Hyperstacks>Stack to Hyperstack...' command.
> You end up with a window with a slider to go through the channels.
> Open the 'channels tool' by hitting ctl+alt "z". Then you can set the
> upper dropdown item in the tool to 'Composite' view. This shows you an
> overlay of the channels and you can uncheck the ones you don't want to
> include. You can pick different color luts for the individual
> channels, the hyperstack is colorcoded in a default manner at the
> beginning.
> Hth
> Christian
>
> ---
> Christian Goosmann
> Mikroskopie
> Max-Planck-Institut für Infektionsbiologie Campus Charité Mitte
> Charitéplatz 1
> 10117 Berlin
> Tel.: +49 30 28460 388
>
> Andy Schofield wrote:
>> Hi All,
>>
>> I have a multiband, 16-bit per band satellite Tiff image and wondered
>> if there are any tools/plugins available in Fiji that enables easy
>> control over switching slices on and off so I can assess the
>> alignment between the different bands (such as the layer control tool
>> in Photoshop etc. for instance)?
>>
>> Regards
>> Andy
>>
>> BTW, in s similar vein, is there a tool/plugin that can manage the
>> selective manual reordering of slices in a stack? I looked at the
>> Image->Stacks->Tools->Stack Sorter but this seemed to be
>> add/remove/duplicate or reverse/order by label only. I ended up
>> renaming each slice to use th reorder by label but wondered if there
>> was plugin that allows the idea of 'Move current slice to slice 6'
>> for instance?
>>
>>
>> The information contained in this message is intended for the
>> addressee only and may contain sensitive information. If you are not
>> the addressee, please delete this message and notify the sender; you
>> should not copy or distribute this message or disclose its contents
>> to anyone. Any views or opinions expressed in this message are those
>> of the individual(s) and not necessarily of the organisation. No
>> reliance may be placed on this message without written confirmation
>> from an authorised representative of its contents. No guarantee is
>> implied that this message or any attachment is virus free or has not
>> been intercepted and amended.
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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The information contained in this message is intended for the addressee only and may contain sensitive information. If you are not the addressee, please delete this message and notify the sender; you should not copy or distribute this message or disclose its contents to anyone. Any views or opinions expressed in this message are those of the individual(s) and not necessarily of the organisation. No reliance may be placed on this message without written confirmation from an authorised representative of its contents. No guarantee is implied that this message or any attachment is virus free or has not been intercepted and amended.


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Re: Correction: Re: Stack control for turning individual slices on and off?

Christian Goosmann-2
Hi Andy
No, sorry. I am not aware of any hidden tool for that. I think you found
a pretty good solution, given that the stack sorter can sort by label. I
linked the command 'Set Label...' to   'F1' as a shortcut key and was
able to edit the labels of a loaded stack quite comfortably (it is
extremely useful to mark the panels via the label if you make a montage
from the stack).
Best
Christian

---
Christian Goosmann
Mikroskopie
Max-Planck-Institut für Infektionsbiologie
Campus Charité Mitte
Charitéplatz 1
10117 Berlin
Tel.: +49 30 28460 388

Andy Schofield wrote:

> Thanks Christian.
>
> That was just what I was after. Switching to the Grayscale view on the Channel Tools dialog box helped a lot too as that meant the channel check boxes were mutually exclusive, enabling the visual 'flicker' between two bands.
>
> On the BTW addendum, any thoughts on that sort of slice control too?
>
> Regards
> Andy
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Christian Goosmann
> Sent: 29 June 2017 12:34
> To: [hidden email]
> Subject: Correction: Re: Stack control for turning individual slices on and off?
>
> Sorry, Ctl+Shift "Z" opens the channels tool of course.
> C.
>
> ---
> Christian Goosmann
> Mikroskopie
> Max-Planck-Institut für Infektionsbiologie Campus Charité Mitte Charitéplatz 1
> 10117 Berlin
> Tel.: +49 30 28460 388
>
> Christian Goosmann wrote:
>> Hi Andy
>> it sounds like you want to load your multiband image as a composite
>> stack in Fiji. If it doesn't automatically import as composite stack,
>> you have to import the single band (or channel) images as a simple
>> stack and use the 'Image>Hyperstacks>Stack to Hyperstack...' command.
>> You end up with a window with a slider to go through the channels.
>> Open the 'channels tool' by hitting ctl+alt "z". Then you can set the
>> upper dropdown item in the tool to 'Composite' view. This shows you an
>> overlay of the channels and you can uncheck the ones you don't want to
>> include. You can pick different color luts for the individual
>> channels, the hyperstack is colorcoded in a default manner at the
>> beginning.
>> Hth
>> Christian
>>
>> ---
>> Christian Goosmann
>> Mikroskopie
>> Max-Planck-Institut für Infektionsbiologie Campus Charité Mitte
>> Charitéplatz 1
>> 10117 Berlin
>> Tel.: +49 30 28460 388
>>
>> Andy Schofield wrote:
>>> Hi All,
>>>
>>> I have a multiband, 16-bit per band satellite Tiff image and wondered
>>> if there are any tools/plugins available in Fiji that enables easy
>>> control over switching slices on and off so I can assess the
>>> alignment between the different bands (such as the layer control tool
>>> in Photoshop etc. for instance)?
>>>
>>> Regards
>>> Andy
>>>
>>> BTW, in s similar vein, is there a tool/plugin that can manage the
>>> selective manual reordering of slices in a stack? I looked at the
>>> Image->Stacks->Tools->Stack Sorter but this seemed to be
>>> add/remove/duplicate or reverse/order by label only. I ended up
>>> renaming each slice to use th reorder by label but wondered if there
>>> was plugin that allows the idea of 'Move current slice to slice 6'
>>> for instance?
>>>
>>>
>>> The information contained in this message is intended for the
>>> addressee only and may contain sensitive information. If you are not
>>> the addressee, please delete this message and notify the sender; you
>>> should not copy or distribute this message or disclose its contents
>>> to anyone. Any views or opinions expressed in this message are those
>>> of the individual(s) and not necessarily of the organisation. No
>>> reliance may be placed on this message without written confirmation
>>> from an authorised representative of its contents. No guarantee is
>>> implied that this message or any attachment is virus free or has not
>>> been intercepted and amended.
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>
> The information contained in this message is intended for the addressee only and may contain sensitive information. If you are not the addressee, please delete this message and notify the sender; you should not copy or distribute this message or disclose its contents to anyone. Any views or opinions expressed in this message are those of the individual(s) and not necessarily of the organisation. No reliance may be placed on this message without written confirmation from an authorised representative of its contents. No guarantee is implied that this message or any attachment is virus free or has not been intercepted and amended.
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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