Software to create raster plot and good combination of VSD and calcium dye

[manojshree]

Dear all,

I was wondering if you could help me to find a decent tool to draw raster plot for the 2-photon images of neuronal network loaded with calcium dye. Which software packages are often used and hopefully free to download except matlab?

Also  which is best voltage sensitive dye one can use in combination with calcium dye (OGB-1/Fluo-4AM/Fura-2AM etc.) ?

Thanks in advance,
Manoj

[Daniel James White]

Hi Manoj,

Ummmm.... i think you mean something like
Image (or the Fiji distribution of ImageJ)
http://pacific.mpi-cbg.de

or do you mean something else?
Can you describe what you mean in more detail?

Dan



On Jun 21, 2010, at 7:03 AM, CONFOCALMICROSCOPY automatic digest system wrote:

> Date:    Sun, 20 Jun 2010 12:04:38 -0400
> From:    manoj jaiswal <[hidden email]>
> Subject: Software to create raster plot and good combination of VSD and calcium dye
>
> --0016363b85da599f2504897858c4
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear all,
>
> I was wondering if you could help me to find a decent tool to draw raster
> plot for the 2-photon images of neuronal network loaded with calcium dye.
> Which software packages are often used and hopefully free to download except
> matlab?
>
> Also  which is best voltage sensitive dye one can use in combination with
> calcium dye (OGB-1/Fluo-4AM/Fura-2AM etc.) ?
>
> Thanks in advance,
> Manoj

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

[phone] (German Mobile)
[phone] (Work phone at MPI-CBG)
[phone] (Fax MPI-CBG LMF)

http://www.bioimagexd.net  BioImageXD
http://pacific.mpi-cbg.de                Fiji -  is just ImageJ (Batteries Included)
http://www.chalkie.org.uk                Dan's Homepages
https://ifn.mpi-cbg.de  Dresden Imaging Facility Network
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )

[manojshree]

Hello Daniel,

Thank you very much for your prompt reply. Here is the few example about Calcium indicator dye loaded neurons, neuronal activity and raster plot publish earlier in journals. I hope this give you a overview about what i am looking to create.


http://www.nature.com/nature/journal/v453/n7198/images/nature06910-f1.2.jpg

http://www.pnas.org/content/104/43/17174/F2.large.jpg

http://www.pnas.org/content/106/46/19557/F4.large.jpg


Thank you
Manoj

On Sun, Jun 20, 2010 at 12:04 PM, manoj jaiswal <[hidden email]> wrote:

Dear all,

I was wondering if you could help me to find a decent tool to draw raster plot for the 2-photon images of neuronal network loaded with calcium dye. Which software packages are often used and hopefully free to download except matlab?

Also  which is best voltage sensitive dye one can use in combination with calcium dye (OGB-1/Fluo-4AM/Fura-2AM etc.) ?

Thanks in advance,
Manoj

[Daniel James White]

Hi manoj 

Should be no problem 

What is your original data format. ? 

Can you sen an example data set? 

D

Daniel J. White Ph.D. 

Max Planck Institute - CBG

Light Microscopy Facility

and Image Processing Facility.

Dresden, Germany.

Fiji is just ImageJ (batteries included)

http://pacific.mpi-cbg.de

BioImageXD 

http://www.bioimagexd.net

http://www.chalkie.org.uk

Mobile [phone]

Office [phone]

[hidden email]

([hidden email])

On 23.06.2010, at 21:29, manoj jaiswal <[hidden email]> wrote:

Hello Daniel,

Thank you very much for your prompt reply. Here is the few example about Calcium indicator dye loaded neurons, neuronal activity and raster plot publish earlier in journals. I hope this give you a overview about what i am looking to create.


http://www.nature.com/nature/journal/v453/n7198/images/nature06910-f1.2.jpg

http://www.pnas.org/content/104/43/17174/F2.large.jpg

http://www.pnas.org/content/106/46/19557/F4.large.jpg


Thank you
Manoj

On Sun, Jun 20, 2010 at 12:04 PM, manoj jaiswal <[hidden email]> wrote:

Dear all,

I was wondering if you could help me to find a decent tool to draw raster plot for the 2-photon images of neuronal network loaded with calcium dye. Which software packages are often used and hopefully free to download except matlab?

Also  which is best voltage sensitive dye one can use in combination with calcium dye (OGB-1/Fluo-4AM/Fura-2AM etc.) ?

Thanks in advance,
Manoj

[ChrisWilms]

Dear Manoj,

I believe what you are looking for is a standard data analysis and  
plotting software. One of the following should do the trick:

Matlab <www.mathworks.com/>
IgorPro <www.wavemetrics.com>
Origin <originlab.com/>
Python <python.org> with SciPy <http://scipy.org/>.

I hope that helps!

Best, Christian

[manojshree]

Hello Christian,

Thanks for your reply,

We do have Origin and  Igor pro but i am not sure if we can make raster plot with these software. I think i need to have mathlab or python for that which not simple and user friendly. I was wondering if there is any commercial software available.

Thanks again for your input.

Best Regards,
Manoj

On Thu, Jun 24, 2010 at 3:01 AM, Christian Wilms <[hidden email]> wrote:

Dear Manoj,

I believe what you are looking for is a standard data analysis and plotting software. One of the following should do the trick:

Matlab <www.mathworks.com/>
IgorPro <www.wavemetrics.com>
Origin <originlab.com/>
Python <python.org> with SciPy <http://scipy.org/>.

I hope that helps!

Best, Christian

[Caroline Bass]

why don't you check out some of the circadian software? I made my own (with help) but the following might do the trick:
 
http://www.circadian.org/softwar.html
 
check out plot, there are probably others out there as well.
 
Caroline

________________________________

From: Confocal Microscopy List on behalf of manoj jaiswal
Sent: Sun 6/27/2010 11:50 PM
To: [hidden email]
Subject: Re: Software to create raster plot and good combination of VSD and calcium dye


Hello Christian,

Thanks for your reply,

We do have Origin and  Igor pro but i am not sure if we can make raster plot with these software. I think i need to have mathlab or python for that which not simple and user friendly. I was wondering if there is any commercial software available.

Thanks again for your input.

Best Regards,
Manoj


On Thu, Jun 24, 2010 at 3:01 AM, Christian Wilms <[hidden email]> wrote:


        Dear Manoj,
       
        I believe what you are looking for is a standard data analysis and plotting software. One of the following should do the trick:
       
        Matlab <www.mathworks.com/>
        IgorPro <www.wavemetrics.com <http://www.wavemetrics.com/> >
        Origin <originlab.com/>
        Python <python.org <http://python.org/> > with SciPy <http://scipy.org/>.
       
        I hope that helps!
       
        Best, Christian
       

[manojshree]

Thanks Caroline,

I will check the link.

Thanks,
Manoj

On Sun, Jun 27, 2010 at 11:55 PM, Caroline Bass <[hidden email]> wrote:

why don't you check out some of the circadian software? I made my own (with help) but the following might do the trick:

http://www.circadian.org/softwar.html

check out plot, there are probably others out there as well.

Caroline

________________________________

From: Confocal Microscopy List on behalf of manoj jaiswal
Sent: Sun 6/27/2010 11:50 PM
To: [hidden email]
Subject: Re: Software to create raster plot and good combination of VSD and calcium dye

Hello Christian,

Thanks for your reply,

We do have Origin and  Igor pro but i am not sure if we can make raster plot with these software. I think i need to have mathlab or python for that which not simple and user friendly. I was wondering if there is any commercial software available.

Thanks again for your input.

Best Regards,
Manoj


On Thu, Jun 24, 2010 at 3:01 AM, Christian Wilms <[hidden email]> wrote:


       Dear Manoj,

       I believe what you are looking for is a standard data analysis and plotting software. One of the following should do the trick:

       Matlab <www.mathworks.com/>

       IgorPro <www.wavemetrics.com <http://www.wavemetrics.com/> >
       Origin <originlab.com/>
       Python <python.org <http://python.org/> > with SciPy <http://scipy.org/>.

       I hope that helps!

       Best, Christian

[Amanda M. Lawrence]

The 2010 Microscopy and Microanalysis meeting is 1 month away and we
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We can*t do it without help from you, so please consider serving as a
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[hidden email]

[ChrisWilms]

Dear Manoj,

> We do have Origin and Igor pro but i am not sure if we can make  
> raster plot with these software. I think i need to have mathlab or  
> python for that which not simple and user friendly. I was wondering  
> if there is any commercial software available.

Without being able to give you a set of procedures for it, I can  
assure you that the plots you sent around as example can all be done  
in Igor Pro, I've done this several times before. For the initial  
steps, you might want to use ImageJ.

I can give you a rough outline of the process. Of course I don't know  
where you are at with the data, so I might cover aspects that you have  
already solved.

1) draw regions of interest and extract intensity traces for each of  
these regions from the image stacks. This is easily done in ImageJ. If  
you need more complex extraction of ROIs, there are methods for this  
(see below for possible solutions).

2) load the intensity traces into Igor Pro, apply the correct wave  
scaling (i.e. your time resolution)

3) you can now simply plot the raw data. There are packages included  
with Igor Pro for using spilt axes, in case you don't want to do that  
by hand.

4) to get the raster, you will need to run an event detection routine.  
Here things get complicated. If you have a good SNR, simple  
thresholding might work. Event detection routines normally used for  
electrophysiological data such as Neuromatic <http://www.neuromatic.thinkrandom.com/Event.html 
 > work really well on fluorescence traces as well. Other routines  
such as those published by Joshua Vogelstein will need to be  
implemented in your programming environment of choice.

5) The event times extracted via the event detection routine are used  
to generate the raster plot.

For a more automated detection of regions of interest, you might want  
to look at the SARIFA package for Igor Pro. I haven't tried it yet  
myself but it looks like it might touch on aspects that could be of  
use to you: <http://www.igorexchange.com/project/SARFIA>

I don't believe there is commercial software available to tackle the  
task. On the other hand, you do have the right tools at your hand  
already :)

For questions on problems you run into with Igor Pro, there is a  
mailing list for that, as well as the discussions on www.igorexchange.com
. I am certain similar resources exist for Origin.

Hope to help,

Christian

[manojshree]

Thank you so much Christian,

Very helpful indeed. Thanks a ton.

Best Regards,
Manoj

On Mon, Jun 28, 2010 at 6:45 AM, Christian Wilms <[hidden email]> wrote:

Dear Manoj,

We do have Origin and Igor pro but i am not sure if we can make raster plot with these software. I think i need to have mathlab or python for that which not simple and user friendly. I was wondering if there is any commercial software available.

Without being able to give you a set of procedures for it, I can assure you that the plots you sent around as example can all be done in Igor Pro, I've done this several times before. For the initial steps, you might want to use ImageJ.

I can give you a rough outline of the process. Of course I don't know where you are at with the data, so I might cover aspects that you have already solved.

1) draw regions of interest and extract intensity traces for each of these regions from the image stacks. This is easily done in ImageJ. If you need more complex extraction of ROIs, there are methods for this (see below for possible solutions).

2) load the intensity traces into Igor Pro, apply the correct wave scaling (i.e. your time resolution)

3) you can now simply plot the raw data. There are packages included with Igor Pro for using spilt axes, in case you don't want to do that by hand.

4) to get the raster, you will need to run an event detection routine. Here things get complicated. If you have a good SNR, simple thresholding might work. Event detection routines normally used for electrophysiological data such as Neuromatic <http://www.neuromatic.thinkrandom.com/Event.html> work really well on fluorescence traces as well. Other routines such as those published by Joshua Vogelstein will need to be implemented in your programming environment of choice.

5) The event times extracted via the event detection routine are used to generate the raster plot.

For a more automated detection of regions of interest, you might want to look at the SARIFA package for Igor Pro. I haven't tried it yet myself but it looks like it might touch on aspects that could be of use to you: <http://www.igorexchange.com/project/SARFIA>

I don't believe there is commercial software available to tackle the task. On the other hand, you do have the right tools at your hand already :)

For questions on problems you run into with Igor Pro, there is a mailing list for that, as well as the discussions on www.igorexchange.com. I am certain similar resources exist for Origin.

Hope to help,

Christian