Re: color deconvolution of histological samples

[Daniel James White]

Hi Alireza

why not post this question to the ImageJ mailing list, where the persons who wrote
the colour deconvolution plugins and who know about histological staining can help you.

i am not super familiar with it...
but a google search will show up lots of information about using imageJ for this kind of analysis.

just do a little home work and come back with some specific questions to the list

cheers

Dan



On Dec 28, 2011, at 5:51 AM, alireza rezai wrote:

> Dear Dr. Dan White,
>
> Happy New Year!
>  
> I would like use ImageJ software and colour deconrolution. I have found you as a Fiji member and specialist in Microscopy and image processing.  My photos are stained by Trichrome Masson, H&E and so IHC. I would like to use imageJ software for them. I am confused for using this software and colour deconrolution forl photos. I do not know how can use it and how can interpret my results. There are so many article have used this software for collagen deposition and cell counts in tissue sections.
> Would you please let me know if you have any information about this method and how can interpret this type of results?
> Your cooperation on this matter is greatly appreciated!
>  
> Best Regards,
> Alireza Rezaeizadeh
>  

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 )

[Vitali Khvatkov-2]

Hi Alireza,

If you search this (ImageJ) forum for color convolution references,
you can find extensive discussion on applicability of color
deconvolution algorithms implemented in ImageJ to Histology stain
systems such as H&E.
In the nutshell:  these algorithms can be useful for some stains and
some application cases, for example for segmentation of IHC nuclear
biomarkers (H&DAB), but applications are limited and you need to
understand limitations to use the algorithms correctly.

If it seems complicated it because it really is.

I know 2 implementations of this ImageJ plugin in free products
besides ImageJ / Fiji:

- Nucleratio /ImmunoMembrane: Institute of Biomedical Technology,
University of Tampere http://imtmicroscope.uta.fi/immunoratio/
- Nucleratio adaptation for Simagis Live platform (our company)
http://portal.sliderocket.com/AXFYY/ImmunoRatio-with-SImagis-Live
(live example: http://apps.simagis.com/live/public/991631a8-5f8e-43cf-8d48-b43a9140e240
)

These products may be easier to use than just plain ImageJ plugin if
they fit your application.

Best,

Vitali Khvatkov
Smart imaging Technologes.Co
[hidden email]
[phone]
live.simagis.com



On Wed, Dec 28, 2011 at 10:15 AM, daniel white <[hidden email]> wrote:

> Hi Alireza
>
> why not post this question to the ImageJ mailing list, where the persons who wrote
> the colour deconvolution plugins and who know about histological staining can help you.
>
> i am not super familiar with it...
> but a google search will show up lots of information about using imageJ for this kind of analysis.
>
> just do a little home work and come back with some specific questions to the list
>
> cheers
>
> Dan
>
>
>
> On Dec 28, 2011, at 5:51 AM, alireza rezai wrote:
>
>> Dear Dr. Dan White,
>>
>> Happy New Year!
>>
>> I would like use ImageJ software and colour deconrolution. I have found you as a Fiji member and specialist in Microscopy and image processing.  My photos are stained by Trichrome Masson, H&E and so IHC. I would like to use imageJ software for them. I am confused for using this software and colour deconrolution forl photos. I do not know how can use it and how can interpret my results. There are so many article have used this software for collagen deposition and cell counts in tissue sections.
>> Would you please let me know if you have any information about this method and how can interpret this type of results?
>> Your cooperation on this matter is greatly appreciated!
>>
>> Best Regards,
>> Alireza Rezaeizadeh
>>
>
> 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 )

[Gabriel Landini]

On Thursday 29 Dec 2011 21:06:38 Vitali Khvatkov wrote:
> I know 2 implementations of this ImageJ plugin in free products
> besides ImageJ / Fiji:
>
> - Nucleratio /ImmunoMembrane: Institute of Biomedical Technology,
> University of Tampere http://imtmicroscope.uta.fi/immunoratio/

I am pretty sure Immunoratio uses the same code of the colour deconvolution
plugin for ImageJ and now included in Fiji, and also uses a number of other
plugins I wrote which are all released under GPL. Immunoratio is (of course)
also released under GPL.

> - Nucleratio adaptation for Simagis Live platform (our company)
> http://portal.sliderocket.com/AXFYY/ImmunoRatio-with-SImagis-Live
> (live example:
> http://apps.simagis.com/live/public/991631a8-5f8e-43cf-8d48-b43a9140e240)

I suppose that the adapted code also conforms to the GPL license of the
original? I am asking because the link provided above does not seem to
acknowledge anything or anybody.

Thanks for any clarification.

Gabriel

[Vitali Khvatkov-2]

Gabriel,

To your question:

We have adopted  ImmunoRatio code without modification of plugins and make
clear reference to the source (see application screenshot)
https://picasaweb.google.com/lh/photo/OIsasY1hlj4lnTC4rL_wRpc8kO0lIPNti3w9
81tk16Y?feat=directlink

As I know, ImmunoRatio team provides links to the source code and
references to GPL licences (they have contacted us specifically with
regard to licence for your plugin)

So yes, the code naturally remains under GPL licence and links to the
source are avaialbe from Immunoratio site.

We do not repackage or redistribute code of Immunoratio or your plugin or
ImageJ, and Immunoratio App is avaialbe on Simagis Live cloud servers at
no charge to any registered users. Anybody can register for free at
http://live.simagis.com/sign-up and request this free App from the
AppStore.

Moreover, we are looking for partnering organization who can provide
server resources to host Simagis Live server with free ImageJ / Fiji apps
for collaborative image analysis as a service to community (we only can
provide 2GB of server space for free)

ImmunoRatio App includes code of several ImagJ plugins, but If you would
like us to provide special attribution to your specific work, can do it -
just send me the attribution statement.

Personally, thank you very much for your work and contribution.  I think
your plugin is the best piece of GPL code avaialbe for implementation of
color deconvolution methods by Ruifrok et al.  I highly recommend it to
anywone looking for GPL implemenation.

Warm Regards,


Vitali Khvatkov
Smart Imaging Technologies
[phone]
www.live.simagis.com




-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Gabriel Landini
Sent: Thursday, December 29, 2011 5:14 PM
To: [hidden email]
Subject: Re: color deconvolution of histological samples

On Thursday 29 Dec 2011 21:06:38 Vitali Khvatkov wrote:
> I know 2 implementations of this ImageJ plugin in free products
> besides ImageJ / Fiji:
>
> - Nucleratio /ImmunoMembrane: Institute of Biomedical Technology,
> University of Tampere http://imtmicroscope.uta.fi/immunoratio/

I am pretty sure Immunoratio uses the same code of the colour
deconvolution plugin for ImageJ and now included in Fiji, and also uses a
number of other plugins I wrote which are all released under GPL.
Immunoratio is (of course) also released under GPL.

> - Nucleratio adaptation for Simagis Live platform (our company)
> http://portal.sliderocket.com/AXFYY/ImmunoRatio-with-SImagis-Live
> (live example:
> http://apps.simagis.com/live/public/991631a8-5f8e-43cf-8d48-b43a9140e2
> 40)

I suppose that the adapted code also conforms to the GPL license of the
original? I am asking because the link provided above does not seem to
acknowledge anything or anybody.

Thanks for any clarification.

Gabriel