Analyze DF/F

[Nicolás Pírez]

Dear users,

I would like to be able to measure the intensity change in a cell body
along a time lapse.
I would like to first threshold the image and from that threshold image run
a plugging to measure the intensity change (multimeasure ??).

I am having trouble being able to automatically select the ROI from the
threshold image. Additionally I would like to be able to correct for small
movement artifacts.

Any help would be greatly appreciated. Let me know if an example image
would be necessary but a bit big.
​
Thanks, Nicolas.​

--
Nicolás Pírez, PhD
[hidden email]
[phone]

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

[Krs5]

Dear Nicolas,

To correct for small movement artefacts (jittery) you could use the Image Stabilizer plugin (http://www.kangli.org/code/Image_Stabilizer.html) or TurboReg plugin (http://bigwww.epfl.ch/thevenaz/turboreg/)

I think without a few sample frames it will be difficult for list members to help with the ROI selection.

Best wishes

Kees

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Nicolás Pírez
Sent: 12 August 2014 18:49
To: [hidden email]
Subject: Analyze DF/F

Dear users,

I would like to be able to measure the intensity change in a cell body along a time lapse.
I would like to first threshold the image and from that threshold image run a plugging to measure the intensity change (multimeasure ??).

I am having trouble being able to automatically select the ROI from the threshold image. Additionally I would like to be able to correct for small movement artifacts.

Any help would be greatly appreciated. Let me know if an example image would be necessary but a bit big.
​
Thanks, Nicolas.​

--
Nicolás Pírez, PhD
[hidden email]
[phone]

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

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

[Nicolás Pírez]

Dear Kees, thanks a lot for your response. I will look at those plugins!

Here I am attaching four consecutive frames that I hope serve as an example
for the ROI I am working on.

Thanks a lot.

Nico.


--
Nicolás Pírez, PhD
[hidden email]
[phone]


On Wed, Aug 13, 2014 at 5:03 AM, Straatman, Kees (Dr.) <[hidden email]
> wrote:

> Dear Nicolas,
>
> To correct for small movement artefacts (jittery) you could use the Image
> Stabilizer plugin (http://www.kangli.org/code/Image_Stabilizer.html) or
> TurboReg plugin (http://bigwww.epfl.ch/thevenaz/turboreg/)
>
> I think without a few sample frames it will be difficult for list members
> to help with the ROI selection.
>
> Best wishes
>
> Kees
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Nicolás Pírez
> Sent: 12 August 2014 18:49
> To: [hidden email]
> Subject: Analyze DF/F
>
> Dear users,
>
> I would like to be able to measure the intensity change in a cell body
> along a time lapse.
> I would like to first threshold the image and from that threshold image
> run a plugging to measure the intensity change (multimeasure ??).
>
> I am having trouble being able to automatically select the ROI from the
> threshold image. Additionally I would like to be able to correct for small
> movement artifacts.
>
> Any help would be greatly appreciated. Let me know if an example image
> would be necessary but a bit big.
> ​
> Thanks, Nicolas.​
>
> --
> Nicolás Pírez, PhD
> [hidden email]
> [phone]
>
> --
> 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

[Mustafa Umut Sarac]

Dear Nico ,

I am not seeing any image attached to your mail<


umut


On Wed, Aug 13, 2014 at 3:26 PM, Nicolás Pírez <[hidden email]>
wrote:

> Dear Kees, thanks a lot for your response. I will look at those plugins!
>
> Here I am attaching four consecutive frames that I hope serve as an example
> for the ROI I am working on.
>
> Thanks a lot.
>
> Nico.
>
>
> --
> Nicolás Pírez, PhD
> [hidden email]
> [phone]
>
>
> On Wed, Aug 13, 2014 at 5:03 AM, Straatman, Kees (Dr.) <
> [hidden email]
> > wrote:
>
> > Dear Nicolas,
> >
> > To correct for small movement artefacts (jittery) you could use the Image
> > Stabilizer plugin (http://www.kangli.org/code/Image_Stabilizer.html) or
> > TurboReg plugin (http://bigwww.epfl.ch/thevenaz/turboreg/)
> >
> > I think without a few sample frames it will be difficult for list members
> > to help with the ROI selection.
> >
> > Best wishes
> >
> > Kees
> >
> > -----Original Message-----
> > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> > Nicolás Pírez
> > Sent: 12 August 2014 18:49
> > To: [hidden email]
> > Subject: Analyze DF/F
> >
> > Dear users,
> >
> > I would like to be able to measure the intensity change in a cell body
> > along a time lapse.
> > I would like to first threshold the image and from that threshold image
> > run a plugging to measure the intensity change (multimeasure ??).
> >
> > I am having trouble being able to automatically select the ROI from the
> > threshold image. Additionally I would like to be able to correct for
> small
> > movement artifacts.
> >
> > Any help would be greatly appreciated. Let me know if an example image
> > would be necessary but a bit big.
> > ​
> > Thanks, Nicolas.​
> >
> > --
> > Nicolás Pírez, PhD
> > [hidden email]
> > [phone]
> >
> > --
> > 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

[Nicolás Pírez]

Dear Umut, that is strange since I am seeing the files as attachments in my
sent mail. Do I need any special authorization to submit an attachment to
the list? Maybe it was bigger than a certain limit?

I will attach one to this message again.

I am sorry for all the noise.

Thanks, Nico.

--
Nicolás Pírez, PhD
[hidden email]
[phone]

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