Colocalization analysis in Fiji/ImageJ Coloc_2 plugin updated with several fixes.

[Daniel James White]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Dear colocalization analysis fans.

Thanks the keen eyes and astute minds of users
(Thanks to all of you!!!)
of the new working prototype
Coloc_2 plugin for Fiji (is just imageJ - batteries included)
we have identified and fixed an number of bugs and design problems in the code:

1) A problem in the design of how regions of interest/mask were implemented
caused a bug in the thresholded Manders coefficient calculation that gave values greater than 1.
This should now be fixed. Please test it as tell us if you feel it does the right thing.  
(JACoP might give different numbers due to a different interpretation of the maths in the original Costes paper.
After asking Dr. Costes, we believe Coloc_2 is correct)

2) Some further fixes were made in how masks/ROIs are handled for the
Costes statistical significance randomization test.

3) We added test code that uses Gaussian shaped spot images of various patterns
as per Manders' original paper, in order to recapitulate his tests and to identify
problems in our implementations of algorithms which calculate Pearsons and Manders coefficients etc.

There are also various little tweaks and redesigns,
that should make it easier for any programmer to read, follow and understand
and then extend the code with new functionality
(Spearman correlation anyone? Objects based analysis like in JACoP - anyone?)

Look in the GIT log to see all the code revision commit messages from Tom and Johannes.
The ideas/design document is still viewable at
https://docs.google.com/document/d/1bEJyXdGyKx4J_G6WlsABpcl3cn-kI5CQs57qU-3Gx7Y/edit


Thanks to all involved,
and please let us know how you would like the user interface and the standardized output PDF to look.

happy colocalizing... update Fiji and you will get the new version of Coloc_2.

cheers

Dan



Dr. Daniel James White BSc. (Hons.) PhD

Leader - Image Processing Facility,
Senior Microscopist,
Light Microscopy Facility.

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)
chalkie666 Skype
http://www.bioimagexd.net  BioImageXD
http://fiji.sc                                        Fiji -  is just ImageJ (Batteries Included)
http://www.chalkie.org.uk                Dan's Homepages
https://ifn.mpi-cbg.de  Biopolis Dresden Imaging Platform (BioDIP)
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )

[George McNamara]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Hi Dan,

Too bad red + green = yellow pixel colocalization and its many
coefficients is dead. See PubMed 21809413 - do you have nearest neighbor
analysis in yet/

George

On 11/2/2011 10:54 AM, Daniel James White wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Dear colocalization analysis fans.
>
> Thanks the keen eyes and astute minds of users
> (Thanks to all of you!!!)
> of the new working prototype
> Coloc_2 plugin for Fiji (is just imageJ - batteries included)
> we have identified and fixed an number of bugs and design problems in the code:
>
> 1) A problem in the design of how regions of interest/mask were implemented
> caused a bug in the thresholded Manders coefficient calculation that gave values greater than 1.
> This should now be fixed. Please test it as tell us if you feel it does the right thing.
> (JACoP might give different numbers due to a different interpretation of the maths in the original Costes paper.
> After asking Dr. Costes, we believe Coloc_2 is correct)
>
> 2) Some further fixes were made in how masks/ROIs are handled for the
> Costes statistical significance randomization test.
>
> 3) We added test code that uses Gaussian shaped spot images of various patterns
> as per Manders' original paper, in order to recapitulate his tests and to identify
> problems in our implementations of algorithms which calculate Pearsons and Manders coefficients etc.
>
> There are also various little tweaks and redesigns,
> that should make it easier for any programmer to read, follow and understand
> and then extend the code with new functionality
> (Spearman correlation anyone? Objects based analysis like in JACoP - anyone?)
>
> Look in the GIT log to see all the code revision commit messages from Tom and Johannes.
> The ideas/design document is still viewable at
> https://docs.google.com/document/d/1bEJyXdGyKx4J_G6WlsABpcl3cn-kI5CQs57qU-3Gx7Y/edit
>
>
> Thanks to all involved,
> and please let us know how you would like the user interface and the standardized output PDF to look.
>
> happy colocalizing... update Fiji and you will get the new version of Coloc_2.
>
> cheers
>
> Dan
>
>
>
> Dr. Daniel James White BSc. (Hons.) PhD
>
> Leader - Image Processing Facility,
> Senior Microscopist,
> Light Microscopy Facility.
>
> 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)
> chalkie666 Skype
> http://www.bioimagexd.net  BioImageXD
> http://fiji.sc                                        Fiji -  is just ImageJ (Batteries Included)
> http://www.chalkie.org.uk                Dan's Homepages
> https://ifn.mpi-cbg.de  Biopolis Dresden Imaging Platform (BioDIP)
> dan (at) chalkie.org.uk
> ( white (at) mpi-cbg.de )
>
>    

--


George McNamara, PhD
Analytical Imaging Core Facility
University of Miami

[Daniel James White]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Hi George,

On Nov 3, 2011, at 6:03 AM, CONFOCALMICROSCOPY automatic digest system wrote:

> Date:    Wed, 2 Nov 2011 22:04:39 -0400
> From:    George McNamara <[hidden email]>
> Subject: Re: Colocalization analysis in Fiji/ImageJ Coloc_2 plugin updated with several fixes.
>
> Hi Dan,
>
> Too bad red + green = yellow pixel colocalization and its many
> coefficients is dead. See PubMed 21809413 - do you have nearest neighbor
> analysis in yet/

No! Do you want to implement it!?

Ha Ha! Long live pixel based intensity correlation colocalization analysis.

Seriously though.... yes this is a sensible method that they outline here...
pity the actually workflow/code they used is nowhere to be seen,
despite the software they used being open source (its from Finland! )
http://csbi.ltdk.helsinki.fi/anduril/site/.

So they got it half right.... the script they used should be published also though... maybe I should ask for them...

General point (which George makes obliquely here)
is that coloc analysis only makes sense if you define the spatial scale you are talking about.

If the universe is 1 single voxel - then everything is colocalised.
If my voxels are smaller than electrons... then _Nothing_ colocalizes!

Pauli's exclusion principle says that 2 particles can't have the same wave mechanical description.
So i cant have 2 atoms in the same place.... So i can't have a GFP and a mCherry in the same place either.

BUT... so long as we define the spatial scale we are measuring the correlations over... ie the
spatial sampling rate and the optical resolution .... which we always should.
Then it does make sense for things to "be" in the same physical location,
so long as they are much smaller then the space scale or resultion we are working in.

Of course, many biological "coloc" problems are actually situations where
the spatial correlation or overlap is never full, rather blobs site "next to" other blobs,
and we need a good method of quantifying that.... how close are the blobs?

.....and the above mentioned paper has a method for that!
Great... so who wants to implement that as a module in Coloc_2
... we tried to make it easy for others to contribute modules...

Spearman correlation anyone?

cheers
Dam

>
> George
>
> On 11/2/2011 10:54 AM, Daniel James White wrote:
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> *****
>>
>> Dear colocalization analysis fans.
>>
>> Thanks the keen eyes and astute minds of users
>> (Thanks to all of you!!!)
>> of the new working prototype
>> Coloc_2 plugin for Fiji (is just imageJ - batteries included)
>> we have identified and fixed an number of bugs and design problems in the code:

Dr. Daniel James White BSc. (Hons.) PhD

Leader - Image Processing Facility,
Senior Microscopist,
Light Microscopy Facility.

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)
chalkie666 Skype
http://www.bioimagexd.net  BioImageXD
http://fiji.sc                                        Fiji -  is just ImageJ (Batteries Included)
http://www.chalkie.org.uk                Dan's Homepages
https://ifn.mpi-cbg.de  Biopolis Dresden Imaging Platform (BioDIP)
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )

[Vitaly Boyko]

Is it (coloc) still hot in the age of single molecu
*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Hi George and Dan,

Is it (coloc) still hot in the age of single molecule fluorescence and raster ICS.

Why not propagating xyztc imaging, which is also supported technologically, where c is biomolecule concentration per voxel?

Cheers,

Vitaly


________________________________
From: Daniel James White <[hidden email]>
To: [hidden email]
Sent: Thursday, November 3, 2011 11:03 AM
Subject: Re: Colocalization analysis in Fiji/ImageJ Coloc_2 plugin updated with several fixes.

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Hi George,

On Nov 3, 2011, at 6:03 AM, CONFOCALMICROSCOPY automatic digest system wrote:

> Date:    Wed, 2 Nov 2011 22:04:39 -0400
> From:    George McNamara <[hidden email]>
> Subject: Re: Colocalization analysis in Fiji/ImageJ Coloc_2 plugin updated with several fixes.
>
> Hi Dan,
>
> Too bad red + green = yellow pixel colocalization and its many
> coefficients is dead. See PubMed 21809413 - do you have nearest neighbor
> analysis in yet/

No! Do you want to implement it!?

Ha Ha! Long live pixel based intensity correlation colocalization analysis.

Seriously though.... yes this is a sensible method that they outline here...
pity the actually workflow/code they used is nowhere to be seen,
despite the software they used being open source (its from Finland! )
http://csbi.ltdk.helsinki.fi/anduril/site/.

So they got it half right.... the script they used should be published also though... maybe I should ask for them...

General point (which George makes obliquely here)
is that coloc analysis only makes sense if you define the spatial scale you are talking about.

If the universe is 1 single voxel - then everything is colocalised.
If my voxels are smaller than electrons... then _Nothing_ colocalizes!

Pauli's exclusion principle says that 2 particles can't have the same wave mechanical description.
So i cant have 2 atoms in the same place.... So i can't have a GFP and a mCherry in the same place either.

BUT... so long as we define the spatial scale we are measuring the correlations over... ie the
spatial sampling rate and the optical resolution .... which we always should.
Then it does make sense for things to "be" in the same physical location,
so long as they are much smaller then the space scale or resultion we are working in.

Of course, many biological "coloc" problems are actually situations where
the spatial correlation or overlap is never full, rather blobs site "next to" other blobs,
and we need a good method of quantifying that.... how close are the blobs?

.....and the above mentioned paper has a method for that!
Great... so who wants to implement that as a module in Coloc_2
... we tried to make it easy for others to contribute modules...

Spearman correlation anyone?

cheers
Dam

>
> George
>
> On 11/2/2011 10:54 AM, Daniel James White wrote:
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> *****
>>
>> Dear colocalization analysis fans.
>>
>> Thanks the keen eyes and astute minds of users
>> (Thanks to all of you!!!)
>> of the new working prototype
>> Coloc_2 plugin for Fiji (is just imageJ - batteries included)
>> we have identified and fixed an number of bugs and design problems in the code:

Dr. Daniel James White BSc. (Hons.) PhD

Leader - Image Processing Facility,
Senior Microscopist,
Light Microscopy Facility.

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)
chalkie666                     Skype
http://www.bioimagexd.net     BioImageXD
http://fiji.sc                    Fiji -  is just ImageJ (Batteries Included)
http://www.chalkie.org.uk        Dan's Homepages
https://ifn.mpi-cbg.de             Biopolis Dresden Imaging Platform (BioDIP)
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )

[George McNamara]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Hi Vitaly,

At the single molecule scale, colocalization is dead. I am now busy
trying to figure out how to get internal funding for simFCS to do Phasor
analysis, re: PMID: 21808026 and PMID: 21858900.

George
p.s. sorry Jay - I am unable to figure out how to use your ImageJ plugin
to do Phasor analysis with B&H SPCm / SPCimage TCSPC FLIM data (I don't
see Phasor in the plugins list of names). I am unsure whether
ImageJ/Bio-Formats is opening the data files correctly (they look pretty
much empty in ImageJ). I tried one of your commands with a FLIM image,
crashed ImageJ.


On 11/3/2011 1:15 PM, Vitaly Boyko wrote:

> Is it (coloc) still hot in the age of single molecu
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi George and Dan,
>
> Is it (coloc) still hot in the age of single molecule fluorescence and raster ICS.
>
> Why not propagating xyztc imaging, which is also supported technologically, where c is biomolecule concentration per voxel?
>
> Cheers,
>
> Vitaly
>
>
> ________________________________
> From: Daniel James White<[hidden email]>
> To: [hidden email]
> Sent: Thursday, November 3, 2011 11:03 AM
> Subject: Re: Colocalization analysis in Fiji/ImageJ Coloc_2 plugin updated with several fixes.
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi George,
>
> On Nov 3, 2011, at 6:03 AM, CONFOCALMICROSCOPY automatic digest system wrote:
>
>    
>> Date:    Wed, 2 Nov 2011 22:04:39 -0400
>> From:    George McNamara<[hidden email]>
>> Subject: Re: Colocalization analysis in Fiji/ImageJ Coloc_2 plugin updated with several fixes.
>>
>> Hi Dan,
>>
>> Too bad red + green = yellow pixel colocalization and its many
>> coefficients is dead. See PubMed 21809413 - do you have nearest neighbor
>> analysis in yet/
>>      
> No! Do you want to implement it!?
>
> Ha Ha! Long live pixel based intensity correlation colocalization analysis.
>
> Seriously though.... yes this is a sensible method that they outline here...
> pity the actually workflow/code they used is nowhere to be seen,
> despite the software they used being open source (its from Finland! )
> http://csbi.ltdk.helsinki.fi/anduril/site/.
>
> So they got it half right.... the script they used should be published also though... maybe I should ask for them...
>
> General point (which George makes obliquely here)
> is that coloc analysis only makes sense if you define the spatial scale you are talking about.
>
> If the universe is 1 single voxel - then everything is colocalised.
> If my voxels are smaller than electrons... then _Nothing_ colocalizes!
>
> Pauli's exclusion principle says that 2 particles can't have the same wave mechanical description.
> So i cant have 2 atoms in the same place.... So i can't have a GFP and a mCherry in the same place either.
>
> BUT... so long as we define the spatial scale we are measuring the correlations over... ie the
> spatial sampling rate and the optical resolution .... which we always should.
> Then it does make sense for things to "be" in the same physical location,
> so long as they are much smaller then the space scale or resultion we are working in.
>
> Of course, many biological "coloc" problems are actually situations where
> the spatial correlation or overlap is never full, rather blobs site "next to" other blobs,
> and we need a good method of quantifying that.... how close are the blobs?
>
> .....and the above mentioned paper has a method for that!
> Great... so who wants to implement that as a module in Coloc_2
> ... we tried to make it easy for others to contribute modules...
>
> Spearman correlation anyone?
>
> cheers
> Dam
>
>
>
>    
>> George
>>
>> On 11/2/2011 10:54 AM, Daniel James White wrote:
>>      
>>> *****
>>> To join, leave or search the confocal microscopy listserv, go to:
>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>>> *****
>>>
>>> Dear colocalization analysis fans.
>>>
>>> Thanks the keen eyes and astute minds of users
>>> (Thanks to all of you!!!)
>>> of the new working prototype
>>> Coloc_2 plugin for Fiji (is just imageJ - batteries included)
>>> we have identified and fixed an number of bugs and design problems in the code:
>>>        
> Dr. Daniel James White BSc. (Hons.) PhD
>
> Leader - Image Processing Facility,
> Senior Microscopist,
> Light Microscopy Facility.
>
> 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)
> chalkie666                     Skype
> http://www.bioimagexd.net     BioImageXD
> http://fiji.sc                    Fiji -  is just ImageJ (Batteries Included)
> http://www.chalkie.org.uk        Dan's Homepages
> https://ifn.mpi-cbg.de             Biopolis Dresden Imaging Platform (BioDIP)
> dan (at) chalkie.org.uk
> ( white (at) mpi-cbg.de )
>
>    

--


George McNamara, PhD
Analytical Imaging Core Facility
University of Miami

[Daniel James White]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Hi George and Vitaly,


On Nov 4, 2011, at 6:02 AM, CONFOCALMICROSCOPY automatic digest system wrote:

> Date:    Thu, 3 Nov 2011 21:14:22 -0400
> From:    George McNamara <[hidden email]>
> Subject: Re: Colocalization analysis in Fiji/ImageJ Coloc_2 plugin updated with several fixes.

> Hi Vitaly,
>
> At the single molecule scale, colocalization is dead.

there never was anything to measure at that scale....
except perhaps a FRET/FLIM measured or other wide measured distance between molecules.

But, lets not get ahead of ourselves....
we can talk about fancy new methods,
but most folks doing biological fluorescence imaging
dont have access to these advanced methods yet,
and very much still rely on looking for yellow stuff (wrong approach at that is)
for colocalization. The first step it got get them using
better analysis methods for the kind of images data they get
from "conventional" confocal and widefield+deconvolution images.
Pixel intensity correlation over space and object based colocalization are still vastly under used.

> I am now busy
> trying to figure out how to get internal funding for simFCS to do Phasor
> analysis, re: PMID: 21808026 and PMID: 21858900.
>
> George
> p.s. sorry Jay - I am unable to figure out how to use your ImageJ plugin
> to do Phasor analysis with B&H SPCm / SPCimage TCSPC FLIM data (I don't
> see Phasor in the plugins list of names). I am unsure whether
> ImageJ/Bio-Formats is opening the data files correctly (they look pretty
> much empty in ImageJ). I tried one of your commands with a FLIM image,
> crashed ImageJ.

If we can get it working,
we can also add it to the Fiji distribution of ImageJ,
so folk just get it and dont have to install anything.

THe plugin author can take ownership of that plugin in Fiji
and maintain it, and its docs.

Documentation can like on the Fiji wiki or linked to an external site from there.

QuickPALM is already there in Fiji, for instance.

cheers

Dan

>
>
> On 11/3/2011 1:15 PM, Vitaly Boyko wrote:
>> Is it (coloc) still hot in the age of single molecu
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> *****
>>
>> Hi George and Dan,
>>
>> Is it (coloc) still hot in the age of single molecule fluorescence and raster ICS.
>>
>> Why not propagating xyztc imaging, which is also supported technologically, where c is biomolecule concentration per voxel?
>>
>> Cheers,
>>
>> Vitaly

Dr. Daniel James White BSc. (Hons.) PhD

Leader - Image Processing Facility,
Senior Microscopist,
Light Microscopy Facility.

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)
chalkie666 Skype
http://www.bioimagexd.net  BioImageXD
http://fiji.sc                                        Fiji -  is just ImageJ (Batteries Included)
http://www.chalkie.org.uk                Dan's Homepages
https://ifn.mpi-cbg.de  Biopolis Dresden Imaging Platform (BioDIP)
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )

[Jeremy Adler-4]

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

It is hard enough to get scientists to make and journals to require  
measurements of colocalization without (George) teasing everyone by  
announcing colocalization is dead.

Hi resolution imaging has not reached molecular resolution, but  
increasing resolution creates some intriguing problems. a) most  
molecules are not inherently fluorescent so we image and localise a  
fluorescent tag that is offset from the target b) stochastic methods  
have their own noise - the probability of a molecule being imaged or  
even reimaged. Molecular Poisson noise will impair nearest neighbour  
analyses as will the presence of untagged molecules.

But back in the imaging world most of us inhabit we should appreciate  
that colocalization measurements divide into two categories, those  
that characterise cooccurence (M1 and M2) and those that characterize  
correlation (Pearson &  Spearman) among the fluorescence that show  
cooccurence. There is third category of coefficients that are  
inherently confusing and perhaps a fourth for coefficients those are  
incorrectly applied.

Adler J., Parmryd I. Cytometry A. 2010, 77(8), 733-42.

In answer to Dan's question including the Spearman correlation  
coefficient is worthwhile, it is unaffected by non linearities and is  
less senstive to outliers than the Pearson correlation coefficient.




Quoting George McNamara <[hidden email]>:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi Dan,
>
> Too bad red + green = yellow pixel colocalization and its many  
> coefficients is dead. See PubMed 21809413 - do you have nearest  
> neighbor analysis in yet/
>
> George
>
> On 11/2/2011 10:54 AM, Daniel James White wrote:
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> *****
>>
>> Dear colocalization analysis fans.
>>
>> Thanks the keen eyes and astute minds of users
>> (Thanks to all of you!!!)
>> of the new working prototype
>> Coloc_2 plugin for Fiji (is just imageJ - batteries included)
>> we have identified and fixed an number of bugs and design problems  
>> in the code:
>>
>> 1) A problem in the design of how regions of interest/mask were implemented
>> caused a bug in the thresholded Manders coefficient calculation  
>> that gave values greater than 1.
>> This should now be fixed. Please test it as tell us if you feel it  
>> does the right thing.
>> (JACoP might give different numbers due to a different  
>> interpretation of the maths in the original Costes paper.
>> After asking Dr. Costes, we believe Coloc_2 is correct)
>>
>> 2) Some further fixes were made in how masks/ROIs are handled for the
>> Costes statistical significance randomization test.
>>
>> 3) We added test code that uses Gaussian shaped spot images of  
>> various patterns
>> as per Manders' original paper, in order to recapitulate his tests  
>> and to identify
>> problems in our implementations of algorithms which calculate  
>> Pearsons and Manders coefficients etc.
>>
>> There are also various little tweaks and redesigns,
>> that should make it easier for any programmer to read, follow and understand
>> and then extend the code with new functionality
>> (Spearman correlation anyone? Objects based analysis like in JACoP  
>> - anyone?)
>>
>> Look in the GIT log to see all the code revision commit messages  
>> from Tom and Johannes.
>> The ideas/design document is still viewable at
>> https://docs.google.com/document/d/1bEJyXdGyKx4J_G6WlsABpcl3cn-kI5CQs57qU-3Gx7Y/edit
>>
>>
>> Thanks to all involved,
>> and please let us know how you would like the user interface and  
>> the standardized output PDF to look.
>>
>> happy colocalizing... update Fiji and you will get the new version  
>> of Coloc_2.
>>
>> cheers
>>
>> Dan
>>
>>
>>
>> Dr. Daniel James White BSc. (Hons.) PhD
>>
>> Leader - Image Processing Facility,
>> Senior Microscopist,
>> Light Microscopy Facility.
>>
>> 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)
>> chalkie666 Skype
>> http://www.bioimagexd.net  BioImageXD
>> http://fiji.sc                                        Fiji -  is just ImageJ (Batteries Included)
>> http://www.chalkie.org.uk                Dan's Homepages
>> https://ifn.mpi-cbg.de  Biopolis Dresden Imaging Platform (BioDIP)
>> dan (at) chalkie.org.uk
>> ( white (at) mpi-cbg.de )
>>
>>
>
>
> --
>
>
> George McNamara, PhD
> Analytical Imaging Core Facility
> University of Miami
>

Jeremy Adler
IGP
Rudbeckslaboratoriet
Daghammersköljdsväg 20
751 85 Uppsala
Sweden

0046 (0)18 471 4607

[Platre Matt]

Hi,

I just want to know where can I find Coloc_2 plugins, if it's possible?
Moreover, does it exist a method for stricly calculate colocalization inside ROI on imageJ.
What are plugings that allow me to do that?
I would like to claculate only intracellular compartement excluding plasma membrane, does it possible?

Thank you,

Matthieu Platre