Automatic quantification of morphological changes in dendrites transsections in electron micrographs

[Laurien]

Dear all,

Does anyone of you have experience measuring the diameter and area of
(transversally cut) dendrites and their myelin sheath in electron
micrographs?
In our otolaryngology-laboratory we calculate these by circumferencing
them manually, which is very time consuming.
Since the (dark stained) dendrites are easy to identify from the (uneven) background, I hope
it's possible to measure the size of axoplasm and thickness of myelin
sheath in a more automatic way.
Also I'd like to measure the packing density by dividing the total
number of dendrites by the area outlined by the bony boundaries.

Is there an efficient way to measure all in an automatic scale?  I'd
appreciate your help since I'm new to processing via ImageJ.


Thank you in advance.

Yours sincerely,

Laurien Waaijer
Medical student,
Utrecht University, The Netherlands

[Cammer, Michael]

Back in the NIH-Image days we had a macro which would automatically segment the dark outer rings and the corresponding white inner axons.  The macro reported the areas of each.  It also fitted these areas to a circle to report the radii of the outer rings of myelin and inner core of axon and to report G ratios.
So it should be easily doable in ImageJ.
_________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: [phone]  Cell: [phone]

________________________________________
From: ImageJ Interest Group [[hidden email]] On Behalf Of Laurien [[hidden email]]
Sent: Monday, May 09, 2011 5:23 AM
To: [hidden email]
Subject: Automatic quantification of morphological changes in dendrites transsections in electron micrographs

Dear all,

Does anyone of you have experience measuring the diameter and area of
(transversally cut) dendrites and their myelin sheath in electron
micrographs?
In our otolaryngology-laboratory we calculate these by circumferencing
them manually, which is very time consuming.
Since the (dark stained) dendrites are easy to identify from the (uneven)
background, I hope
it's possible to measure the size of axoplasm and thickness of myelin
sheath in a more automatic way.
Also I'd like to measure the packing density by dividing the total
number of dendrites by the area outlined by the bony boundaries.

Is there an efficient way to measure all in an automatic scale?  I'd
appreciate your help since I'm new to processing via ImageJ.


Thank you in advance.

Yours sincerely,

Laurien Waaijer
Medical student,
Utrecht University, The Netherlands

--
View this message in context: http://imagej.588099.n2.nabble.com/Automatic-quantification-of-morphological-changes-in-dendrites-transsections-in-electron-micrographs-tp6343598p6343598.html
Sent from the ImageJ mailing list archive at Nabble.com.

------------------------------------------------------------
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=================================

[paul_rostand]

hi Michael,

I am a new imagej user,

I am also interested in a  macro which would automatically do the segmentation, but in the oder way round. that means  detect the the dark innner  rings and the corresponding white outer axons. Where can I find this macro? I want to adapt it to the study of my laser welding process, the pictures are looking similar to myelin ones.

regards

paul Rostand

universität Erlangen Germany

---

De : "Cammer, Michael [via ImageJ]" <[hidden email]>
À : paul_rostand <[hidden email]>
Envoyé le : Lun 9 mai 2011, 20h 31min 16s
Objet : Re: Automatic quantification of morphological changes in dendrites transsections in electron micrographs

Back in the NIH-Image days we had a macro which would automatically segment the dark outer rings and the corresponding white inner axons.  The macro reported the areas of each.  It also fitted these areas to a circle to report the radii of the outer rings of myelin and inner core of axon and to report G ratios.
So it should be easily doable in ImageJ.
_________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: [phone]  Cell: [phone]

________________________________________
From: ImageJ Interest Group [[hidden email]] On Behalf Of Laurien [[hidden email]]
Sent: Monday, May 09, 2011 5:23 AM
To: [hidden email]
Subject: Automatic quantification of morphological changes in dendrites transsections in electron micrographs

Dear all,

Does anyone of you have experience measuring the diameter and area of
(transversally cut) dendrites and their myelin sheath in electron
micrographs?
In our otolaryngology-laboratory we calculate these by circumferencing
them manually, which is very time consuming.
Since the (dark stained) dendrites are easy to identify from the (uneven)
background, I hope
it's possible to measure the size of axoplasm and thickness of myelin
sheath in a more automatic way.
Also I'd like to measure the packing density by dividing the total
number of dendrites by the area outlined by the bony boundaries.

Is there an efficient way to measure all in an automatic scale?  I'd
appreciate your help since I'm new to processing via ImageJ.


Thank you in advance.

Yours sincerely,

Laurien Waaijer
Medical student,
Utrecht University, The Netherlands

--
View this message in context: http://imagej.588099.n2.nabble.com/Automatic-quantification-of-morphological-changes-in-dendrites-transsections-in-electron-micrographs-tp6343598p6343598.html
Sent from the ImageJ mailing list archive at Nabble.com.

------------------------------------------------------------
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=================================

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[Laurien]

Unfortunately I can't find the macro on the ImageJ site, or did you
mean that you used to use a 'homemade' macro, Michael?

Paul, I'm now trying a manual way of counting which is faster than
completely manually circumferencing the areas. Maybe it can be usefull
for you:

I've used the option to smooth the (grayscale, 8-bit) image, enhance
contrast and then invert the image, use a treshold to exclude the
background --> save it as pic2.
Then I use Image Calculator and substract the original pic from pic 2.
By now the 'background noise' is reduced, but I smoothen the picture
even more by using the ' despeckle' function.
Then I set the Otsu-treshold to leave the myelin sheaths unmarked.
Then I use the magic wand en use ctrl-t to add the marked sessions to
the ROI manager. Then repeat this process for the inner myelin ring to
select the axoplasm.

Now I have to find an easy way to substract the inner ring from the
outer ring per cell. I haven't selected the ROI (outer circle and
inner circle) per cell, but more randomly (first a couple of outer
rings, then a couple of inner rings), so there not in order in the
ROImanager.
My idea would be to use the ROI's without the original picture, fill
the ring between inner and outer circle up with a color and then count
the pixels per particle?

Or do you have an example of the macro you used Michael?

Thank you in advance, I really appreciate your help,

Yours sincerely,

Laurien Waaijer
University Utrecht


2011/5/10 paul_rostand [via ImageJ]
<[hidden email]>:

> hi Michael,
> I am a new imagej user,
> I am also interested in a  macro which would automatically do the
> segmentation, but in the oder way round. that means  detect the the dark
> innner  rings and the corresponding white outer axons. Where can I find this
> macro? I want to adapt it to the study of my laser welding process, the
> pictures are looking similar to myelin ones.
> regards
> paul Rostand
> universität Erlangen Germany
> ________________________________
> De : "Cammer, Michael [via ImageJ]" <[hidden email]>
> À : paul_rostand <[hidden email]>
> Envoyé le : Lun 9 mai 2011, 20h 31min 16s
> Objet : Re: Automatic quantification of morphological changes in dendrites
> transsections in electron micrographs
>
> Back in the NIH-Image days we had a macro which would automatically segment
> the dark outer rings and the corresponding white inner axons.  The macro
> reported the areas of each.  It also fitted these areas to a circle to
> report the radii of the outer rings of myelin and inner core of axon and to
> report G ratios.
> So it should be easily doable in ImageJ.
> _________________________________________
> Michael Cammer, Assistant Research Scientist
> Skirball Institute of Biomolecular Medicine
> Lab: [phone]  Cell: [phone]
>
> ________________________________________
> From: ImageJ Interest Group [[hidden email]] On Behalf Of Laurien [[hidden
> email]]
> Sent: Monday, May 09, 2011 5:23 AM
> To: [hidden email]
> Subject: Automatic quantification of morphological changes in dendrites
> transsections in electron micrographs
>
> Dear all,
>
> Does anyone of you have experience measuring the diameter and area of
> (transversally cut) dendrites and their myelin sheath in electron
> micrographs?
> In our otolaryngology-laboratory we calculate these by circumferencing
> them manually, which is very time consuming.
> Since the (dark stained) dendrites are easy to identify from the (uneven)
> background, I hope
> it's possible to measure the size of axoplasm and thickness of myelin
> sheath in a more automatic way.
> Also I'd like to measure the packing density by dividing the total
> number of dendrites by the area outlined by the bony boundaries.
>
> Is there an efficient way to measure all in an automatic scale?  I'd
> appreciate your help since I'm new to processing via ImageJ.
>
>
> Thank you in advance.
>
> Yours sincerely,
>
> Laurien Waaijer
> Medical student,
> Utrecht University, The Netherlands
>
> --
> View this message in context:
> http://imagej.588099.n2.nabble.com/Automatic-quantification-of-morphological-changes-in-dendrites-transsections-in-electron-micrographs-tp6343598p6343598.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> ------------------------------------------------------------
> This email message, including any attachments, is for the sole use of the
> intended recipient(s) and may contain information that is proprietary,
> confidential, and exempt from disclosure under applicable law. Any
> unauthorized review, use, disclosure, or distribution is prohibited. If you
> have received this email in error please notify the sender by return email
> and delete the original message. Please note, the recipient should check
> this email and any attachments for the presence of viruses. The organization
> accepts no liability for any damage caused by any virus transmitted by this
> email.
> =================================
>
>
> ________________________________
> If you reply to this email, your message will be added to the discussion
> below:
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> To start a new topic under ImageJ, email [hidden email]
> To unsubscribe from ImageJ, click here.
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> To unsubscribe from Automatic quantification of morphological changes in
> dendrites transsections in electron micrographs, click here.

[melkor2.0]

Hi, I need something similar, I have confocal images of the soma of neurons,
and I want to analyze the number of puncta in close vicinity with the plasma
membrane. I would like to draw manually the perimeter of the soma and imageJ
to select the area within 5 microns from my selection. I think is not
possible to ImageJ to do it automatically, so how can I make a "ring"
selection? I would like to crop that selection and then run another macro.
Thanks,

ramon

On 10 May 2011 10:26, Laurien Waaijer <[hidden email]> wrote:

> Unfortunately I can't find the macro on the ImageJ site, or did you
> mean that you used to use a 'homemade' macro, Michael?
>
> Paul, I'm now trying a manual way of counting which is faster than
> completely manually circumferencing the areas. Maybe it can be usefull
> for you:
>
> I've used the option to smooth the (grayscale, 8-bit) image, enhance
> contrast and then invert the image, use a treshold to exclude the
> background --> save it as pic2.
> Then I use Image Calculator and substract the original pic from pic 2.
> By now the 'background noise' is reduced, but I smoothen the picture
> even more by using the ' despeckle' function.
> Then I set the Otsu-treshold to leave the myelin sheaths unmarked.
> Then I use the magic wand en use ctrl-t to add the marked sessions to
> the ROI manager. Then repeat this process for the inner myelin ring to
> select the axoplasm.
>
> Now I have to find an easy way to substract the inner ring from the
> outer ring per cell. I haven't selected the ROI (outer circle and
> inner circle) per cell, but more randomly (first a couple of outer
> rings, then a couple of inner rings), so there not in order in the
> ROImanager.
> My idea would be to use the ROI's without the original picture, fill
> the ring between inner and outer circle up with a color and then count
> the pixels per particle?
>
> Or do you have an example of the macro you used Michael?
>
> Thank you in advance, I really appreciate your help,
>
> Yours sincerely,
>
> Laurien Waaijer
> University Utrecht
>
>
> 2011/5/10 paul_rostand [via ImageJ]
> <[hidden email]>:
> > hi Michael,
> > I am a new imagej user,
> > I am also interested in a  macro which would automatically do the
> > segmentation, but in the oder way round. that means  detect the the dark
> > innner  rings and the corresponding white outer axons. Where can I find
> this
> > macro? I want to adapt it to the study of my laser welding process, the
> > pictures are looking similar to myelin ones.
> > regards
> > paul Rostand
> > universität Erlangen Germany
> > ________________________________
> > De : "Cammer, Michael [via ImageJ]" <[hidden email]>
> > À : paul_rostand <[hidden email]>
> > Envoyé le : Lun 9 mai 2011, 20h 31min 16s
> > Objet : Re: Automatic quantification of morphological changes in
> dendrites
> > transsections in electron micrographs
> >
> > Back in the NIH-Image days we had a macro which would automatically
> segment
> > the dark outer rings and the corresponding white inner axons.  The macro
> > reported the areas of each.  It also fitted these areas to a circle to
> > report the radii of the outer rings of myelin and inner core of axon and
> to
> > report G ratios.
> > So it should be easily doable in ImageJ.
> > _________________________________________
> > Michael Cammer, Assistant Research Scientist
> > Skirball Institute of Biomolecular Medicine
> > Lab: [phone]  Cell: [phone]
> >
> > ________________________________________
> > From: ImageJ Interest Group [[hidden email]] On Behalf Of Laurien
> [[hidden
> > email]]
> > Sent: Monday, May 09, 2011 5:23 AM
> > To: [hidden email]
> > Subject: Automatic quantification of morphological changes in dendrites
> > transsections in electron micrographs
> >
> > Dear all,
> >
> > Does anyone of you have experience measuring the diameter and area of
> > (transversally cut) dendrites and their myelin sheath in electron
> > micrographs?
> > In our otolaryngology-laboratory we calculate these by circumferencing
> > them manually, which is very time consuming.
> > Since the (dark stained) dendrites are easy to identify from the (uneven)
> > background, I hope
> > it's possible to measure the size of axoplasm and thickness of myelin
> > sheath in a more automatic way.
> > Also I'd like to measure the packing density by dividing the total
> > number of dendrites by the area outlined by the bony boundaries.
> >
> > Is there an efficient way to measure all in an automatic scale?  I'd
> > appreciate your help since I'm new to processing via ImageJ.
> >
> >
> > Thank you in advance.
> >
> > Yours sincerely,
> >
> > Laurien Waaijer
> > Medical student,
> > Utrecht University, The Netherlands
> >
> > --
> > View this message in context:
> >
> http://imagej.588099.n2.nabble.com/Automatic-quantification-of-morphological-changes-in-dendrites-transsections-in-electron-micrographs-tp6343598p6343598.html
> > Sent from the ImageJ mailing list archive at Nabble.com.
> >
> > ------------------------------------------------------------
> > This email message, including any attachments, is for the sole use of the
> > intended recipient(s) and may contain information that is proprietary,
> > confidential, and exempt from disclosure under applicable law. Any
> > unauthorized review, use, disclosure, or distribution is prohibited. If
> you
> > have received this email in error please notify the sender by return
> email
> > and delete the original message. Please note, the recipient should check
> > this email and any attachments for the presence of viruses. The
> organization
> > accepts no liability for any damage caused by any virus transmitted by
> this
> > email.
> > =================================
> >
> >
> > ________________________________
> > If you reply to this email, your message will be added to the discussion
> > below:
> >
> http://imagej.588099.n2.nabble.com/Automatic-quantification-of-morphological-changes-in-dendrites-transsections-in-electron-micrographs-tp6343598p6345260.html
> > To start a new topic under ImageJ, email [hidden email]
> > To unsubscribe from ImageJ, click here.
> >
> > ________________________________
> > If you reply to this email, your message will be added to the discussion
> > below:
> >
> http://imagej.588099.n2.nabble.com/Automatic-quantification-of-morphological-changes-in-dendrites-transsections-in-electron-micrographs-tp6343598p6346737.html
> > To unsubscribe from Automatic quantification of morphological changes in
> > dendrites transsections in electron micrographs, click here.
>

[lechristophe]

You can use this

Draw your selection
Store it in the ROI manager
Edit>Selection> Enlarge command with a negative number to shrink your ROI
(the distance is in pixels, so you have to convert from microns)
Store the shrunk ROI in the ROI manager
Substract the second ROI from the first one by selecting both in the ROI
manager and More...>XOR
You'll get your "ring" ROI

Christophe

On Tue, May 10, 2011 at 10:46, Ramon <[hidden email]> wrote:

> Hi, I need something similar, I have confocal images of the soma of
> neurons,
> and I want to analyze the number of puncta in close vicinity with the
> plasma
> membrane. I would like to draw manually the perimeter of the soma and
> imageJ
> to select the area within 5 microns from my selection. I think is not
> possible to ImageJ to do it automatically, so how can I make a "ring"
> selection? I would like to crop that selection and then run another macro.
> Thanks,
>
> ramon
>
> On 10 May 2011 10:26, Laurien Waaijer <[hidden email]> wrote:
>
> > Unfortunately I can't find the macro on the ImageJ site, or did you
> > mean that you used to use a 'homemade' macro, Michael?
> >
> > Paul, I'm now trying a manual way of counting which is faster than
> > completely manually circumferencing the areas. Maybe it can be usefull
> > for you:
> >
> > I've used the option to smooth the (grayscale, 8-bit) image, enhance
> > contrast and then invert the image, use a treshold to exclude the
> > background --> save it as pic2.
> > Then I use Image Calculator and substract the original pic from pic 2.
> > By now the 'background noise' is reduced, but I smoothen the picture
> > even more by using the ' despeckle' function.
> > Then I set the Otsu-treshold to leave the myelin sheaths unmarked.
> > Then I use the magic wand en use ctrl-t to add the marked sessions to
> > the ROI manager. Then repeat this process for the inner myelin ring to
> > select the axoplasm.
> >
> > Now I have to find an easy way to substract the inner ring from the
> > outer ring per cell. I haven't selected the ROI (outer circle and
> > inner circle) per cell, but more randomly (first a couple of outer
> > rings, then a couple of inner rings), so there not in order in the
> > ROImanager.
> > My idea would be to use the ROI's without the original picture, fill
> > the ring between inner and outer circle up with a color and then count
> > the pixels per particle?
> >
> > Or do you have an example of the macro you used Michael?
> >
> > Thank you in advance, I really appreciate your help,
> >
> > Yours sincerely,
> >
> > Laurien Waaijer
> > University Utrecht
> >
> >
> > 2011/5/10 paul_rostand [via ImageJ]
> > <[hidden email]>:
> > > hi Michael,
> > > I am a new imagej user,
> > > I am also interested in a  macro which would automatically do the
> > > segmentation, but in the oder way round. that means  detect the the
> dark
> > > innner  rings and the corresponding white outer axons. Where can I find
> > this
> > > macro? I want to adapt it to the study of my laser welding process, the
> > > pictures are looking similar to myelin ones.
> > > regards
> > > paul Rostand
> > > universität Erlangen Germany
> > > ________________________________
> > > De : "Cammer, Michael [via ImageJ]" <[hidden email]>
> > > À : paul_rostand <[hidden email]>
> > > Envoyé le : Lun 9 mai 2011, 20h 31min 16s
> > > Objet : Re: Automatic quantification of morphological changes in
> > dendrites
> > > transsections in electron micrographs
> > >
> > > Back in the NIH-Image days we had a macro which would automatically
> > segment
> > > the dark outer rings and the corresponding white inner axons.  The
> macro
> > > reported the areas of each.  It also fitted these areas to a circle to
> > > report the radii of the outer rings of myelin and inner core of axon
> and
> > to
> > > report G ratios.
> > > So it should be easily doable in ImageJ.
> > > _________________________________________
> > > Michael Cammer, Assistant Research Scientist
> > > Skirball Institute of Biomolecular Medicine
> > > Lab: [phone]  Cell: [phone]
> > >
> > > ________________________________________
> > > From: ImageJ Interest Group [[hidden email]] On Behalf Of Laurien
> > [[hidden
> > > email]]
> > > Sent: Monday, May 09, 2011 5:23 AM
> > > To: [hidden email]
> > > Subject: Automatic quantification of morphological changes in dendrites
> > > transsections in electron micrographs
> > >
> > > Dear all,
> > >
> > > Does anyone of you have experience measuring the diameter and area of
> > > (transversally cut) dendrites and their myelin sheath in electron
> > > micrographs?
> > > In our otolaryngology-laboratory we calculate these by circumferencing
> > > them manually, which is very time consuming.
> > > Since the (dark stained) dendrites are easy to identify from the
> (uneven)
> > > background, I hope
> > > it's possible to measure the size of axoplasm and thickness of myelin
> > > sheath in a more automatic way.
> > > Also I'd like to measure the packing density by dividing the total
> > > number of dendrites by the area outlined by the bony boundaries.
> > >
> > > Is there an efficient way to measure all in an automatic scale?  I'd
> > > appreciate your help since I'm new to processing via ImageJ.
> > >
> > >
> > > Thank you in advance.
> > >
> > > Yours sincerely,
> > >
> > > Laurien Waaijer
> > > Medical student,
> > > Utrecht University, The Netherlands
> > >
> > > --
> > > View this message in context:
> > >
> >
> http://imagej.588099.n2.nabble.com/Automatic-quantification-of-morphological-changes-in-dendrites-transsections-in-electron-micrographs-tp6343598p6343598.html
> > > Sent from the ImageJ mailing list archive at Nabble.com.
> > >
> > > ------------------------------------------------------------
> > > This email message, including any attachments, is for the sole use of
> the
> > > intended recipient(s) and may contain information that is proprietary,
> > > confidential, and exempt from disclosure under applicable law. Any
> > > unauthorized review, use, disclosure, or distribution is prohibited. If
> > you
> > > have received this email in error please notify the sender by return
> > email
> > > and delete the original message. Please note, the recipient should
> check
> > > this email and any attachments for the presence of viruses. The
> > organization
> > > accepts no liability for any damage caused by any virus transmitted by
> > this
> > > email.
> > > =================================
> > >
> > >
> > > ________________________________
> > > If you reply to this email, your message will be added to the
> discussion
> > > below:
> > >
> >
> http://imagej.588099.n2.nabble.com/Automatic-quantification-of-morphological-changes-in-dendrites-transsections-in-electron-micrographs-tp6343598p6345260.html
> > > To start a new topic under ImageJ, email [hidden email]
> > > To unsubscribe from ImageJ, click here.
> > >
> > > ________________________________
> > > If you reply to this email, your message will be added to the
> discussion
> > > below:
> > >
> >
> http://imagej.588099.n2.nabble.com/Automatic-quantification-of-morphological-changes-in-dendrites-transsections-in-electron-micrographs-tp6343598p6346737.html
> > > To unsubscribe from Automatic quantification of morphological changes
> in
> > > dendrites transsections in electron micrographs, click here.
> >
>

[Laurien]

Thanks for your help, Christophe.
The problem with this command is that it requires one pixel number,
which I don't have, because my 'inner ring' differences according to
each cell. From these ' donuts' (myelin sheaths) I'd like to measure
the thickness and the surface. Since I've already managed to outline
the inner and outer layer as ROIs, all I have to do is substract them
from eachother.
One solution could maybe be selecting the outer layers first, make a
ROI-set of them and then selecting the inner layers and make a second
ROI-set.. Then I can maybe make a mask or something with them?

Another problem I'm facing is that I can't figure out how to 'select
all' ROIs from my list, does anyone know how to do this?

Regards,

Laurien Waaijer
University Utrecht

2011/5/10 Christophe Leterrier <[hidden email]>:

> You can use this
>
> Draw your selection
> Store it in the ROI manager
> Edit>Selection> Enlarge command with a negative number to shrink your ROI
> (the distance is in pixels, so you have to convert from microns)
> Store the shrunk ROI in the ROI manager
> Substract the second ROI from the first one by selecting both in the ROI
> manager and More...>XOR
> You'll get your "ring" ROI
>
> Christophe
>
> On Tue, May 10, 2011 at 10:46, Ramon <[hidden email]> wrote:
>
>> Hi, I need something similar, I have confocal images of the soma of
>> neurons,
>> and I want to analyze the number of puncta in close vicinity with the
>> plasma
>> membrane. I would like to draw manually the perimeter of the soma and
>> imageJ
>> to select the area within 5 microns from my selection. I think is not
>> possible to ImageJ to do it automatically, so how can I make a "ring"
>> selection? I would like to crop that selection and then run another macro.
>> Thanks,
>>
>> ramon
>>
>> On 10 May 2011 10:26, Laurien Waaijer <[hidden email]> wrote:
>>
>> > Unfortunately I can't find the macro on the ImageJ site, or did you
>> > mean that you used to use a 'homemade' macro, Michael?
>> >
>> > Paul, I'm now trying a manual way of counting which is faster than
>> > completely manually circumferencing the areas. Maybe it can be usefull
>> > for you:
>> >
>> > I've used the option to smooth the (grayscale, 8-bit) image, enhance
>> > contrast and then invert the image, use a treshold to exclude the
>> > background --> save it as pic2.
>> > Then I use Image Calculator and substract the original pic from pic 2.
>> > By now the 'background noise' is reduced, but I smoothen the picture
>> > even more by using the ' despeckle' function.
>> > Then I set the Otsu-treshold to leave the myelin sheaths unmarked.
>> > Then I use the magic wand en use ctrl-t to add the marked sessions to
>> > the ROI manager. Then repeat this process for the inner myelin ring to
>> > select the axoplasm.
>> >
>> > Now I have to find an easy way to substract the inner ring from the
>> > outer ring per cell. I haven't selected the ROI (outer circle and
>> > inner circle) per cell, but more randomly (first a couple of outer
>> > rings, then a couple of inner rings), so there not in order in the
>> > ROImanager.
>> > My idea would be to use the ROI's without the original picture, fill
>> > the ring between inner and outer circle up with a color and then count
>> > the pixels per particle?
>> >
>> > Or do you have an example of the macro you used Michael?
>> >
>> > Thank you in advance, I really appreciate your help,
>> >
>> > Yours sincerely,
>> >
>> > Laurien Waaijer
>> > University Utrecht
>> >
>> >
>> > 2011/5/10 paul_rostand [via ImageJ]
>> > <[hidden email]>:
>> > > hi Michael,
>> > > I am a new imagej user,
>> > > I am also interested in a  macro which would automatically do the
>> > > segmentation, but in the oder way round. that means  detect the the
>> dark
>> > > innner  rings and the corresponding white outer axons. Where can I find
>> > this
>> > > macro? I want to adapt it to the study of my laser welding process, the
>> > > pictures are looking similar to myelin ones.
>> > > regards
>> > > paul Rostand
>> > > universität Erlangen Germany
>> > > ________________________________
>> > > De : "Cammer, Michael [via ImageJ]" <[hidden email]>
>> > > À : paul_rostand <[hidden email]>
>> > > Envoyé le : Lun 9 mai 2011, 20h 31min 16s
>> > > Objet : Re: Automatic quantification of morphological changes in
>> > dendrites
>> > > transsections in electron micrographs
>> > >
>> > > Back in the NIH-Image days we had a macro which would automatically
>> > segment
>> > > the dark outer rings and the corresponding white inner axons.  The
>> macro
>> > > reported the areas of each.  It also fitted these areas to a circle to
>> > > report the radii of the outer rings of myelin and inner core of axon
>> and
>> > to
>> > > report G ratios.
>> > > So it should be easily doable in ImageJ.
>> > > _________________________________________
>> > > Michael Cammer, Assistant Research Scientist
>> > > Skirball Institute of Biomolecular Medicine
>> > > Lab: [phone]  Cell: [phone]
>> > >
>> > > ________________________________________
>> > > From: ImageJ Interest Group [[hidden email]] On Behalf Of Laurien
>> > [[hidden
>> > > email]]
>> > > Sent: Monday, May 09, 2011 5:23 AM
>> > > To: [hidden email]
>> > > Subject: Automatic quantification of morphological changes in dendrites
>> > > transsections in electron micrographs
>> > >
>> > > Dear all,
>> > >
>> > > Does anyone of you have experience measuring the diameter and area of
>> > > (transversally cut) dendrites and their myelin sheath in electron
>> > > micrographs?
>> > > In our otolaryngology-laboratory we calculate these by circumferencing
>> > > them manually, which is very time consuming.
>> > > Since the (dark stained) dendrites are easy to identify from the
>> (uneven)
>> > > background, I hope
>> > > it's possible to measure the size of axoplasm and thickness of myelin
>> > > sheath in a more automatic way.
>> > > Also I'd like to measure the packing density by dividing the total
>> > > number of dendrites by the area outlined by the bony boundaries.
>> > >
>> > > Is there an efficient way to measure all in an automatic scale?  I'd
>> > > appreciate your help since I'm new to processing via ImageJ.
>> > >
>> > >
>> > > Thank you in advance.
>> > >
>> > > Yours sincerely,
>> > >
>> > > Laurien Waaijer
>> > > Medical student,
>> > > Utrecht University, The Netherlands
>> > >
>> > > --
>> > > View this message in context:
>> > >
>> >
>> http://imagej.588099.n2.nabble.com/Automatic-quantification-of-morphological-changes-in-dendrites-transsections-in-electron-micrographs-tp6343598p6343598.html
>> > > Sent from the ImageJ mailing list archive at Nabble.com.
>> > >
>> > > ------------------------------------------------------------
>> > > This email message, including any attachments, is for the sole use of
>> the
>> > > intended recipient(s) and may contain information that is proprietary,
>> > > confidential, and exempt from disclosure under applicable law. Any
>> > > unauthorized review, use, disclosure, or distribution is prohibited. If
>> > you
>> > > have received this email in error please notify the sender by return
>> > email
>> > > and delete the original message. Please note, the recipient should
>> check
>> > > this email and any attachments for the presence of viruses. The
>> > organization
>> > > accepts no liability for any damage caused by any virus transmitted by
>> > this
>> > > email.
>> > > =================================
>> > >
>> > >
>> > > ________________________________
>> > > If you reply to this email, your message will be added to the
>> discussion
>> > > below:
>> > >
>> >
>> http://imagej.588099.n2.nabble.com/Automatic-quantification-of-morphological-changes-in-dendrites-transsections-in-electron-micrographs-tp6343598p6345260.html
>> > > To start a new topic under ImageJ, email [hidden email]
>> > > To unsubscribe from ImageJ, click here.
>> > >
>> > > ________________________________
>> > > If you reply to this email, your message will be added to the
>> discussion
>> > > below:
>> > >
>> >
>> http://imagej.588099.n2.nabble.com/Automatic-quantification-of-morphological-changes-in-dendrites-transsections-in-electron-micrographs-tp6343598p6346737.html
>> > > To unsubscribe from Automatic quantification of morphological changes
>> in
>> > > dendrites transsections in electron micrographs, click here.
>> >
>>
>

[David Strachan]

Hi Laurien,

On a windows system you can use the <shift> or the <ctrl> key and then click on entries in ROI manager and you can select multiple ROI's

Regards

David Strachan


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Laurien Waaijer
Sent: 10 May 2011 10:48
To: [hidden email]
Subject: Re: Re : Automatic quantification of morphological changes in dendrites transsections in electron micrographs

Thanks for your help, Christophe.
The problem with this command is that it requires one pixel number, which I don't have, because my 'inner ring' differences according to each cell. From these ' donuts' (myelin sheaths) I'd like to measure the thickness and the surface. Since I've already managed to outline the inner and outer layer as ROIs, all I have to do is substract them from eachother.
One solution could maybe be selecting the outer layers first, make a ROI-set of them and then selecting the inner layers and make a second ROI-set.. Then I can maybe make a mask or something with them?

Another problem I'm facing is that I can't figure out how to 'select all' ROIs from my list, does anyone know how to do this?

Regards,

Laurien Waaijer
University Utrecht

2011/5/10 Christophe Leterrier <[hidden email]>:

> You can use this
>
> Draw your selection
> Store it in the ROI manager
> Edit>Selection> Enlarge command with a negative number to shrink your
> Edit>Selection> ROI
> (the distance is in pixels, so you have to convert from microns) Store
> the shrunk ROI in the ROI manager Substract the second ROI from the
> first one by selecting both in the ROI manager and More...>XOR You'll
> get your "ring" ROI
>
> Christophe
>
> On Tue, May 10, 2011 at 10:46, Ramon <[hidden email]> wrote:
>
>> Hi, I need something similar, I have confocal images of the soma of
>> neurons, and I want to analyze the number of puncta in close vicinity
>> with the plasma membrane. I would like to draw manually the perimeter
>> of the soma and imageJ to select the area within 5 microns from my
>> selection. I think is not possible to ImageJ to do it automatically,
>> so how can I make a "ring"
>> selection? I would like to crop that selection and then run another macro.
>> Thanks,
>>
>> ramon
>>
>> On 10 May 2011 10:26, Laurien Waaijer <[hidden email]> wrote:
>>
>> > Unfortunately I can't find the macro on the ImageJ site, or did you
>> > mean that you used to use a 'homemade' macro, Michael?
>> >
>> > Paul, I'm now trying a manual way of counting which is faster than
>> > completely manually circumferencing the areas. Maybe it can be
>> > usefull for you:
>> >
>> > I've used the option to smooth the (grayscale, 8-bit) image,
>> > enhance contrast and then invert the image, use a treshold to
>> > exclude the background --> save it as pic2.
>> > Then I use Image Calculator and substract the original pic from pic 2.
>> > By now the 'background noise' is reduced, but I smoothen the
>> > picture even more by using the ' despeckle' function.
>> > Then I set the Otsu-treshold to leave the myelin sheaths unmarked.
>> > Then I use the magic wand en use ctrl-t to add the marked sessions
>> > to the ROI manager. Then repeat this process for the inner myelin
>> > ring to select the axoplasm.
>> >
>> > Now I have to find an easy way to substract the inner ring from the
>> > outer ring per cell. I haven't selected the ROI (outer circle and
>> > inner circle) per cell, but more randomly (first a couple of outer
>> > rings, then a couple of inner rings), so there not in order in the
>> > ROImanager.
>> > My idea would be to use the ROI's without the original picture,
>> > fill the ring between inner and outer circle up with a color and
>> > then count the pixels per particle?
>> >
>> > Or do you have an example of the macro you used Michael?
>> >
>> > Thank you in advance, I really appreciate your help,
>> >
>> > Yours sincerely,
>> >
>> > Laurien Waaijer
>> > University Utrecht
>> >
>> >
>> > 2011/5/10 paul_rostand [via ImageJ]
>> > <[hidden email]>:
>> > > hi Michael,
>> > > I am a new imagej user,
>> > > I am also interested in a  macro which would automatically do the
>> > > segmentation, but in the oder way round. that means  detect the
>> > > the
>> dark
>> > > innner  rings and the corresponding white outer axons. Where can
>> > > I find
>> > this
>> > > macro? I want to adapt it to the study of my laser welding
>> > > process, the pictures are looking similar to myelin ones.
>> > > regards
>> > > paul Rostand
>> > > universität Erlangen Germany
>> > > ________________________________
>> > > De : "Cammer, Michael [via ImageJ]" <[hidden email]> À :
>> > > paul_rostand <[hidden email]> Envoyé le : Lun 9 mai 2011, 20h
>> > > 31min 16s Objet : Re: Automatic quantification of morphological
>> > > changes in
>> > dendrites
>> > > transsections in electron micrographs
>> > >
>> > > Back in the NIH-Image days we had a macro which would
>> > > automatically
>> > segment
>> > > the dark outer rings and the corresponding white inner axons.  
>> > > The
>> macro
>> > > reported the areas of each.  It also fitted these areas to a
>> > > circle to report the radii of the outer rings of myelin and inner
>> > > core of axon
>> and
>> > to
>> > > report G ratios.
>> > > So it should be easily doable in ImageJ.
>> > > _________________________________________
>> > > Michael Cammer, Assistant Research Scientist Skirball Institute
>> > > of Biomolecular Medicine
>> > > Lab: [phone]  Cell: [phone]
>> > >
>> > > ________________________________________
>> > > From: ImageJ Interest Group [[hidden email]] On Behalf Of Laurien
>> > [[hidden
>> > > email]]
>> > > Sent: Monday, May 09, 2011 5:23 AM
>> > > To: [hidden email]
>> > > Subject: Automatic quantification of morphological changes in
>> > > dendrites transsections in electron micrographs
>> > >
>> > > Dear all,
>> > >
>> > > Does anyone of you have experience measuring the diameter and
>> > > area of (transversally cut) dendrites and their myelin sheath in
>> > > electron micrographs?
>> > > In our otolaryngology-laboratory we calculate these by
>> > > circumferencing them manually, which is very time consuming.
>> > > Since the (dark stained) dendrites are easy to identify from the
>> (uneven)
>> > > background, I hope
>> > > it's possible to measure the size of axoplasm and thickness of
>> > > myelin sheath in a more automatic way.
>> > > Also I'd like to measure the packing density by dividing the
>> > > total number of dendrites by the area outlined by the bony boundaries.
>> > >
>> > > Is there an efficient way to measure all in an automatic scale?  
>> > > I'd appreciate your help since I'm new to processing via ImageJ.
>> > >
>> > >
>> > > Thank you in advance.
>> > >
>> > > Yours sincerely,
>> > >
>> > > Laurien Waaijer
>> > > Medical student,
>> > > Utrecht University, The Netherlands
>> > >
>> > > --
>> > > View this message in context:
>> > >
>> >
>> http://imagej.588099.n2.nabble.com/Automatic-quantification-of-morpho
>> logical-changes-in-dendrites-transsections-in-electron-micrographs-tp
>> 6343598p6343598.html
>> > > Sent from the ImageJ mailing list archive at Nabble.com.
>> > >
>> > > ------------------------------------------------------------
>> > > This email message, including any attachments, is for the sole
>> > > use of
>> the
>> > > intended recipient(s) and may contain information that is
>> > > proprietary, confidential, and exempt from disclosure under
>> > > applicable law. Any unauthorized review, use, disclosure, or
>> > > distribution is prohibited. If
>> > you
>> > > have received this email in error please notify the sender by
>> > > return
>> > email
>> > > and delete the original message. Please note, the recipient
>> > > should
>> check
>> > > this email and any attachments for the presence of viruses. The
>> > organization
>> > > accepts no liability for any damage caused by any virus
>> > > transmitted by
>> > this
>> > > email.
>> > > =================================
>> > >
>> > >
>> > > ________________________________
>> > > If you reply to this email, your message will be added to the
>> discussion
>> > > below:
>> > >
>> >
>> http://imagej.588099.n2.nabble.com/Automatic-quantification-of-morpho
>> logical-changes-in-dendrites-transsections-in-electron-micrographs-tp
>> 6343598p6345260.html
>> > > To start a new topic under ImageJ, email [hidden email] To
>> > > unsubscribe from ImageJ, click here.
>> > >
>> > > ________________________________
>> > > If you reply to this email, your message will be added to the
>> discussion
>> > > below:
>> > >
>> >
>> http://imagej.588099.n2.nabble.com/Automatic-quantification-of-morpho
>> logical-changes-in-dendrites-transsections-in-electron-micrographs-tp
>> 6343598p6346737.html
>> > > To unsubscribe from Automatic quantification of morphological
>> > > changes
>> in
>> > > dendrites transsections in electron micrographs, click here.
>> >
>>
>