Combining two max projection images with a 'transparency sliding rule'?

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Combining two max projection images with a 'transparency sliding rule'?

Antonio G. Valdecasas
Hi.

I have a stack of confocal images. As I go through the z axis, some
structures appear that are partially covered by some overlaying surface.

I did two partial maximum projection and would like to create a single
image showing the whole structure.  As the intensity of the first max proj
is higher than the second, composing both is not a good solution.

I remember that there was a software that combined two images and with a
sliding rule one could vary the 'transparency of either image and get a
good solution.

My question is: is there any plugin with something similar to a
'transparency sliding rule' in Fiji/ImageJ?

Thank you in advance for any help.

Best

Antonio

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Re: Combining two max projection images with a 'transparency sliding rule'?

vbindoka
activate the ClearVolume plugin [Help/Update/Manage Update Sites; check
clearvolume].

It has ability to toggle channels on/off, plus opacity sliders per color.

[clearvolume is fussy about graphics cards, however]

cheers,

Vytas


On 8/18/2017 7:44 AM, Antonio G. Valdecasas wrote:

> Hi.
>
> I have a stack of confocal images. As I go through the z axis, some
> structures appear that are partially covered by some overlaying surface.
>
> I did two partial maximum projection and would like to create a single
> image showing the whole structure.  As the intensity of the first max proj
> is higher than the second, composing both is not a good solution.
>
> I remember that there was a software that combined two images and with a
> sliding rule one could vary the 'transparency of either image and get a
> good solution.
>
> My question is: is there any plugin with something similar to a
> 'transparency sliding rule' in Fiji/ImageJ?
>
> Thank you in advance for any help.
>
> Best
>
> Antonio
>
> --
> ImageJ mailing list: https://urldefense.proofpoint.com/v2/url?u=http-3A__imagej.nih.gov_ij_list.html&d=DwIBaQ&c=Nd1gv_ZWYNIRyZYZmXb18oVfc3lTqv2smA_esABG70U&r=pD-sSh_e9cMzytxHgN9Gfakl4sCheZunFOz7i3o-Ewk&m=X2ujGcA0wkKFUzrUxOYhSPJhlxE1YBB0JMY2MnVIYd8&s=GbOuUPPLmrvK-l6iYCsXxtwBNFwTcwYJeMPd6M6RT-s&e=

--
__

Vytas Bindokas, Ph.D.
Research Assoc. Prof.,
Director, BSD Light Microscopy Core Facility
phone: 773-702-4875 [alt's: 773-834-9040 or 773-834-2639]

      [address for letters ONLY (see shipping addr below):]
Dept Pharmacol Physiol Sci MC0926
947 E 58th Street
The University of Chicago
Chicago IL 60637
Room Abbott 129


shipping address (main KCBD site):
V. Bindokas
900 E 57th Street
KCBD room 1250, Microscopy Core
The University of Chicago
Chicago IL 60637


email [hidden email]
web site for LMCF:
http://digital.uchicago.edu

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Re: Combining two max projection images with a 'transparency sliding rule'?

Antonio G. Valdecasas
Thank you very much, Vytas.

However, my version of Fiji/ImageJ       'Help >Update'  does not
leads to 'Manage
Update Sites'. I have updated the Fiji/ImageJ version from a link in
ClearVolume webpage with same result.

Looking at the ClearVolume  page I realize that the instalation of this
plugin is a bit more complex than simply downloading a *.jar file in the
plugin folder.

Any additonal help would be greatly appreciated.

Best

Antonio

2017-08-18 16:23 GMT+02:00 vbindokas <[hidden email]>:

> activate the ClearVolume plugin [Help/Update/Manage Update Sites; check
> clearvolume].
>
> It has ability to toggle channels on/off, plus opacity sliders per color.
>
> [clearvolume is fussy about graphics cards, however]
>
> cheers,
>
> Vytas
>
>
>
> On 8/18/2017 7:44 AM, Antonio G. Valdecasas wrote:
>
>> Hi.
>>
>> I have a stack of confocal images. As I go through the z axis, some
>> structures appear that are partially covered by some overlaying surface.
>>
>> I did two partial maximum projection and would like to create a single
>> image showing the whole structure.  As the intensity of the first max proj
>> is higher than the second, composing both is not a good solution.
>>
>> I remember that there was a software that combined two images and with a
>> sliding rule one could vary the 'transparency of either image and get a
>> good solution.
>>
>> My question is: is there any plugin with something similar to a
>> 'transparency sliding rule' in Fiji/ImageJ?
>>
>> Thank you in advance for any help.
>>
>> Best
>>
>> Antonio
>>
>> --
>> ImageJ mailing list: https://urldefense.proofpoint.
>> com/v2/url?u=http-3A__imagej.nih.gov_ij_list.html&d=DwIBaQ&c
>> =Nd1gv_ZWYNIRyZYZmXb18oVfc3lTqv2smA_esABG70U&r=pD-sSh_e9cMzy
>> txHgN9Gfakl4sCheZunFOz7i3o-Ewk&m=X2ujGcA0wkKFUzrUxOYhSPJh
>> lxE1YBB0JMY2MnVIYd8&s=GbOuUPPLmrvK-l6iYCsXxtwBNFwTcwYJeMPd6M6RT-s&e=
>>
>
> --
> __
>
> Vytas Bindokas, Ph.D.
> Research Assoc. Prof.,
> Director, BSD Light Microscopy Core Facility
> phone: 773-702-4875 [alt's: 773-834-9040 or 773-834-2639]
>
>      [address for letters ONLY (see shipping addr below):]
> Dept Pharmacol Physiol Sci MC0926
> 947 E 58th Street
> The University of Chicago
> Chicago IL 60637
> Room Abbott 129
>
>
> shipping address (main KCBD site):
> V. Bindokas
> 900 E 57th Street
> KCBD room 1250, Microscopy Core
> The University of Chicago
> Chicago IL 60637
>
>
> email [hidden email]
> web site for LMCF:
> http://digital.uchicago.edu
>
> --
> 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: Combining two max projection images with a 'transparency sliding rule'?

ctrueden
Hi Antonio,

> However, my version of Fiji/ImageJ 'Help >Update' does not leads to
> 'Manage Update Sites'.

Are you sure you are choosing "Update..." and not "Update ImageJ..."?

Did you read the documentation?
  https://imagej.net/Following_an_update_site#Add_update_sites

> Looking at the ClearVolume  page I realize that the instalation of
> this plugin is a bit more complex than simply downloading a *.jar file
> in the plugin folder.

It is six clicks:

* Help
* Update...
* "Manage Update Sites" button
* "ClearVolume" checkbox
* Close button
* "Apply changes" button

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 Sat, Aug 19, 2017 at 11:10 AM, Antonio G. Valdecasas <[hidden email]>
wrote:

> Thank you very much, Vytas.
>
> However, my version of Fiji/ImageJ       'Help >Update'  does not
> leads to 'Manage
> Update Sites'. I have updated the Fiji/ImageJ version from a link in
> ClearVolume webpage with same result.
>
> Looking at the ClearVolume  page I realize that the instalation of this
> plugin is a bit more complex than simply downloading a *.jar file in the
> plugin folder.
>
> Any additonal help would be greatly appreciated.
>
> Best
>
> Antonio
>
> 2017-08-18 16:23 GMT+02:00 vbindokas <[hidden email]>:
>
> > activate the ClearVolume plugin [Help/Update/Manage Update Sites; check
> > clearvolume].
> >
> > It has ability to toggle channels on/off, plus opacity sliders per color.
> >
> > [clearvolume is fussy about graphics cards, however]
> >
> > cheers,
> >
> > Vytas
> >
> >
> >
> > On 8/18/2017 7:44 AM, Antonio G. Valdecasas wrote:
> >
> >> Hi.
> >>
> >> I have a stack of confocal images. As I go through the z axis, some
> >> structures appear that are partially covered by some overlaying surface.
> >>
> >> I did two partial maximum projection and would like to create a single
> >> image showing the whole structure.  As the intensity of the first max
> proj
> >> is higher than the second, composing both is not a good solution.
> >>
> >> I remember that there was a software that combined two images and with a
> >> sliding rule one could vary the 'transparency of either image and get a
> >> good solution.
> >>
> >> My question is: is there any plugin with something similar to a
> >> 'transparency sliding rule' in Fiji/ImageJ?
> >>
> >> Thank you in advance for any help.
> >>
> >> Best
> >>
> >> Antonio
> >>
> >> --
> >> ImageJ mailing list: https://urldefense.proofpoint.
> >> com/v2/url?u=http-3A__imagej.nih.gov_ij_list.html&d=DwIBaQ&c
> >> =Nd1gv_ZWYNIRyZYZmXb18oVfc3lTqv2smA_esABG70U&r=pD-sSh_e9cMzy
> >> txHgN9Gfakl4sCheZunFOz7i3o-Ewk&m=X2ujGcA0wkKFUzrUxOYhSPJh
> >> lxE1YBB0JMY2MnVIYd8&s=GbOuUPPLmrvK-l6iYCsXxtwBNFwTcwYJeMPd6M6RT-s&e=
> >>
> >
> > --
> > __
> >
> > Vytas Bindokas, Ph.D.
> > Research Assoc. Prof.,
> > Director, BSD Light Microscopy Core Facility
> > phone: 773-702-4875 [alt's: 773-834-9040 or 773-834-2639]
> >
> >      [address for letters ONLY (see shipping addr below):]
> > Dept Pharmacol Physiol Sci MC0926
> > 947 E 58th Street
> > The University of Chicago
> > Chicago IL 60637
> > Room Abbott 129
> >
> >
> > shipping address (main KCBD site):
> > V. Bindokas
> > 900 E 57th Street
> > KCBD room 1250, Microscopy Core
> > The University of Chicago
> > Chicago IL 60637
> >
> >
> > email [hidden email]
> > web site for LMCF:
> > http://digital.uchicago.edu
> >
> > --
> > 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
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Re: Combining two max projection images with a 'transparency sliding rule'?

Antonio G. Valdecasas
Thank you very much, Curtis.

I had overlooked the 'Manage Update Site' button at the left down corner!!

Best

Antonio

2017-08-20 13:03 GMT+02:00 Curtis Rueden <[hidden email]>:

> Hi Antonio,
>
> > However, my version of Fiji/ImageJ 'Help >Update' does not leads to
> > 'Manage Update Sites'.
>
> Are you sure you are choosing "Update..." and not "Update ImageJ..."?
>
> Did you read the documentation?
>   https://imagej.net/Following_an_update_site#Add_update_sites
>
> > Looking at the ClearVolume  page I realize that the instalation of
> > this plugin is a bit more complex than simply downloading a *.jar file
> > in the plugin folder.
>
> It is six clicks:
>
> * Help
> * Update...
> * "Manage Update Sites" button
> * "ClearVolume" checkbox
> * Close button
> * "Apply changes" button
>
> 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 Sat, Aug 19, 2017 at 11:10 AM, Antonio G. Valdecasas <[hidden email]
> >
> wrote:
>
> > Thank you very much, Vytas.
> >
> > However, my version of Fiji/ImageJ       'Help >Update'  does not
> > leads to 'Manage
> > Update Sites'. I have updated the Fiji/ImageJ version from a link in
> > ClearVolume webpage with same result.
> >
> > Looking at the ClearVolume  page I realize that the instalation of this
> > plugin is a bit more complex than simply downloading a *.jar file in the
> > plugin folder.
> >
> > Any additonal help would be greatly appreciated.
> >
> > Best
> >
> > Antonio
> >
> > 2017-08-18 16:23 GMT+02:00 vbindokas <[hidden email]>:
> >
> > > activate the ClearVolume plugin [Help/Update/Manage Update Sites; check
> > > clearvolume].
> > >
> > > It has ability to toggle channels on/off, plus opacity sliders per
> color.
> > >
> > > [clearvolume is fussy about graphics cards, however]
> > >
> > > cheers,
> > >
> > > Vytas
> > >
> > >
> > >
> > > On 8/18/2017 7:44 AM, Antonio G. Valdecasas wrote:
> > >
> > >> Hi.
> > >>
> > >> I have a stack of confocal images. As I go through the z axis, some
> > >> structures appear that are partially covered by some overlaying
> surface.
> > >>
> > >> I did two partial maximum projection and would like to create a single
> > >> image showing the whole structure.  As the intensity of the first max
> > proj
> > >> is higher than the second, composing both is not a good solution.
> > >>
> > >> I remember that there was a software that combined two images and
> with a
> > >> sliding rule one could vary the 'transparency of either image and get
> a
> > >> good solution.
> > >>
> > >> My question is: is there any plugin with something similar to a
> > >> 'transparency sliding rule' in Fiji/ImageJ?
> > >>
> > >> Thank you in advance for any help.
> > >>
> > >> Best
> > >>
> > >> Antonio
> > >>
> > >> --
> > >> ImageJ mailing list: https://urldefense.proofpoint.
> > >> com/v2/url?u=http-3A__imagej.nih.gov_ij_list.html&d=DwIBaQ&c
> > >> =Nd1gv_ZWYNIRyZYZmXb18oVfc3lTqv2smA_esABG70U&r=pD-sSh_e9cMzy
> > >> txHgN9Gfakl4sCheZunFOz7i3o-Ewk&m=X2ujGcA0wkKFUzrUxOYhSPJh
> > >> lxE1YBB0JMY2MnVIYd8&s=GbOuUPPLmrvK-l6iYCsXxtwBNFwTcwYJeMPd6M6RT-s&e=
> > >>
> > >
> > > --
> > > __
> > >
> > > Vytas Bindokas, Ph.D.
> > > Research Assoc. Prof.,
> > > Director, BSD Light Microscopy Core Facility
> > > phone: 773-702-4875 [alt's: 773-834-9040 or 773-834-2639]
> > >
> > >      [address for letters ONLY (see shipping addr below):]
> > > Dept Pharmacol Physiol Sci MC0926
> > > 947 E 58th Street
> > > The University of Chicago
> > > Chicago IL 60637
> > > Room Abbott 129
> > >
> > >
> > > shipping address (main KCBD site):
> > > V. Bindokas
> > > 900 E 57th Street
> > > KCBD room 1250, Microscopy Core
> > > The University of Chicago
> > > Chicago IL 60637
> > >
> > >
> > > email [hidden email]
> > > web site for LMCF:
> > > http://digital.uchicago.edu
> > >
> > > --
> > > 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
>

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