Image Processing Software

[Ramshesh, Venkat K]

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Dear all,

Our imaging core is looking to buy imaging software for offline image processing, quantification etc. for mostly confocal and multiphoton fluorescence microscopy. I was hoping if folks here had any suggestions or recommendations as to which software to purchase in this regard. Thanks for all your help in advance.

Best,
Venkat

Venkat Ramshesh, PhD
Research Instructor/Facility Manager
Department of Pharmaceutical and Biomedical Scinces and Hollings Cancer Center
Drug Discovery Bldg. DD 507
70 President Street, MSC 140
MUSC, Charleston, SC 29425
Ph: 8438762363
Fax:[phone]
E-mail: [hidden email]

[John Oreopoulos]

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Try ImageJ. It's free:

http://rsbweb.nih.gov/ij/

John Oreopoulos
Research Assistant
Spectral Applied Research
Richmond Hill, Ontario
Canada


On 2011-09-22, at 11:39 AM, Ramshesh, Venkat K wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Dear all,
>
> Our imaging core is looking to buy imaging software for offline image processing, quantification etc. for mostly confocal and multiphoton fluorescence microscopy. I was hoping if folks here had any suggestions or recommendations as to which software to purchase in this regard. Thanks for all your help in advance.
>
> Best,
> Venkat
>
> Venkat Ramshesh, PhD
> Research Instructor/Facility Manager
> Department of Pharmaceutical and Biomedical Scinces and Hollings Cancer Center
> Drug Discovery Bldg. DD 507
> 70 President Street, MSC 140
> MUSC, Charleston, SC 29425
> Ph: 8438762363
> Fax:[phone]
> E-mail: [hidden email]

[Anda Cornea]

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I absolutely agree.

Anda Cornea, Ph.D.
Director of the Imaging and Morphology Core
Oregon National Primate Research Center
503-690-5293


-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of John Oreopoulos
Sent: Thursday, September 22, 2011 1:24 PM
To: [hidden email]
Subject: Re: Image Processing Software

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*****

Try ImageJ. It's free:

http://rsbweb.nih.gov/ij/

John Oreopoulos
Research Assistant
Spectral Applied Research
Richmond Hill, Ontario
Canada


On 2011-09-22, at 11:39 AM, Ramshesh, Venkat K wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Dear all,
>
> Our imaging core is looking to buy imaging software for offline image processing, quantification etc. for mostly confocal and multiphoton fluorescence microscopy. I was hoping if folks here had any suggestions or recommendations as to which software to purchase in this regard. Thanks for all your help in advance.
>
> Best,
> Venkat
>
> Venkat Ramshesh, PhD
> Research Instructor/Facility Manager
> Department of Pharmaceutical and Biomedical Scinces and Hollings
> Cancer Center Drug Discovery Bldg. DD 507
> 70 President Street, MSC 140
> MUSC, Charleston, SC 29425
> Ph: 8438762363
> Fax:[phone]
> E-mail: [hidden email]

[abhijit debroy]

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Image J is very versatile for most image processing operations. If you would
want more specific functions like deconvolution etc, look at specific
softwares (volocity etc.). Image J also has some deconvolution plug ins
available for free.

Abhijit Deb Roy
Biomedical Sciences Program
University of Connecticut Health Centre
PhD Candidate

On Thu, Sep 22, 2011 at 4:56 PM, Anda Cornea <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> I absolutely agree.
>
> Anda Cornea, Ph.D.
> Director of the Imaging and Morphology Core
> Oregon National Primate Research Center
> 503-690-5293
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]]
> On Behalf Of John Oreopoulos
> Sent: Thursday, September 22, 2011 1:24 PM
> To: [hidden email]
> Subject: Re: Image Processing Software
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Try ImageJ. It's free:
>
> http://rsbweb.nih.gov/ij/
>
> John Oreopoulos
> Research Assistant
> Spectral Applied Research
> Richmond Hill, Ontario
> Canada
>
>
> On 2011-09-22, at 11:39 AM, Ramshesh, Venkat K wrote:
>
> > *****
> > To join, leave or search the confocal microscopy listserv, go to:
> > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> > *****
> >
> > Dear all,
> >
> > Our imaging core is looking to buy imaging software for offline image
> processing, quantification etc. for mostly confocal and multiphoton
> fluorescence microscopy. I was hoping if folks here had any suggestions or
> recommendations as to which software to purchase in this regard. Thanks for
> all your help in advance.
> >
> > Best,
> > Venkat
> >
> > Venkat Ramshesh, PhD
> > Research Instructor/Facility Manager
> > Department of Pharmaceutical and Biomedical Scinces and Hollings
> > Cancer Center Drug Discovery Bldg. DD 507
> > 70 President Street, MSC 140
> > MUSC, Charleston, SC 29425
> > Ph: 8438762363
> > Fax:[phone]
> > E-mail: [hidden email]
>

--

[Tim Feinstein-2]

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In favor of ImageJ:
* free, designed by and for imaging scientists.  
* most basic analytical functions are available as plug-ins and/or incorporated into the (also free) Fiji package.  
* difficult to do nonlinear brightness modification (gamma, curves).  Most users do not know that this is not an accepted image manipulation in many contexts and can get you in trouble with journals.  Gamma/curve adjustment is trivially easy in other apps like Photoshop.  

On the minus side:
* Stripped-down user interface.  It may take some patience/training for a new user to get the most out of it.  
* Advanced techniques like deconvolution and 3D presentation or analysis are best done with proprietary software.  
* Many microscope makers package pretty good presentation/analysis software with their system, e.g. Zen for Zeiss, Elements for Nikon.  This is often much more user-friendly.  

In general I'd say that everyone should have it.  The dollar and memory cost are basically nil.  

CellProfiler is another free software specifically designed to enable high-throughput image analysis.  e.g., automatic segmentation (finding the edge of cells) and measurement of cell area, fluorescence intensity/evenness/object number/size/percent mitotic/apoptotic etc etc etc.  I have not used it much but people who do automated siRNA phenotype detection (imaging hundreds of cell micro-colonies on a glass slide, each transfected with a different siRNA) often swear by it.  

For deconvolution there are several competing apps, each of which costs quite a bit.  I tested Autoquant and Huygens and chose the latter, although Autoquant is also excellent.  Both of those also offer quality 3D rendering and analysis, as does Volocity, which I have had a positive experience with in the past.  

best of luck,


TF

Timothy Feinstein, PhD
Postdoctoral Fellow
Laboratory for GPCR Biology
Dept. of Pharmacology & Chemical Biology
University of Pittsburgh, School of Medicine
BST W1301, 200 Lothrop St.
Pittsburgh, PA  15261

On Sep 22, 2011, at 5:39 PM, abhijit debroy wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Image J is very versatile for most image processing operations. If you would
> want more specific functions like deconvolution etc, look at specific
> softwares (volocity etc.). Image J also has some deconvolution plug ins
> available for free.
>
> Abhijit Deb Roy
> Biomedical Sciences Program
> University of Connecticut Health Centre
> PhD Candidate
>
> On Thu, Sep 22, 2011 at 4:56 PM, Anda Cornea <[hidden email]> wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> *****
>>
>> I absolutely agree.
>>
>> Anda Cornea, Ph.D.
>> Director of the Imaging and Morphology Core
>> Oregon National Primate Research Center
>> 503-690-5293
>>
>>
>> -----Original Message-----
>> From: Confocal Microscopy List [mailto:[hidden email]]
>> On Behalf Of John Oreopoulos
>> Sent: Thursday, September 22, 2011 1:24 PM
>> To: [hidden email]
>> Subject: Re: Image Processing Software
>>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> *****
>>
>> Try ImageJ. It's free:
>>
>> http://rsbweb.nih.gov/ij/
>>
>> John Oreopoulos
>> Research Assistant
>> Spectral Applied Research
>> Richmond Hill, Ontario
>> Canada
>>
>>
>> On 2011-09-22, at 11:39 AM, Ramshesh, Venkat K wrote:
>>
>>> *****
>>> To join, leave or search the confocal microscopy listserv, go to:
>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>>> *****
>>>
>>> Dear all,
>>>
>>> Our imaging core is looking to buy imaging software for offline image
>> processing, quantification etc. for mostly confocal and multiphoton
>> fluorescence microscopy. I was hoping if folks here had any suggestions or
>> recommendations as to which software to purchase in this regard. Thanks for
>> all your help in advance.
>>>
>>> Best,
>>> Venkat
>>>
>>> Venkat Ramshesh, PhD
>>> Research Instructor/Facility Manager
>>> Department of Pharmaceutical and Biomedical Scinces and Hollings
>>> Cancer Center Drug Discovery Bldg. DD 507
>>> 70 President Street, MSC 140
>>> MUSC, Charleston, SC 29425
>>> Ph: 8438762363
>>> Fax:[phone]
>>> E-mail: [hidden email]
>>
>
>
>
> --

[mahogny]

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On Thu, 2011-09-22 at 16:23 -0400, John Oreopoulos wrote:
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Try ImageJ. It's free:
>
> http://rsbweb.nih.gov/ij/
>

and use OMERO for image storage
http://www.openmicroscopy.org

and why not also have a look at

http://www.endrov.net

while you are at it. open source image processing is making great
strides at the moment; there is no reason to throw money at the
commercial offerings. if you have money to spare, you get more for it by
improving our open source software!

/Johan

[Johannes Schindelin]

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Dear Tim,

On Thu, 22 Sep 2011, Tim Feinstein wrote:

> [talking about ImageJ]
>
> * difficult to do nonlinear brightness modification (gamma, curves).  
>   Most users do not know that this is not an accepted image manipulation
>   in many contexts and can get you in trouble with journals.  
>   Gamma/curve adjustment is trivially easy in other apps like Photoshop.

Note that it is not _that_ difficult to do in ImageJ. But I do agree with
journals not accepting images manipulated in that way. See e.g.
http://www.uab.edu/researchintegrityandimages/guidelines/list.html. It is
not exhaustive but gives beginners an idea what to watch out for.

In general, however, I would like to see journals accepting only articles
together with the raw data and the method used to process them. After all,
we want to be able to reproduce the results.

> * Advanced techniques like deconvolution and 3D presentation or analysis
>   are best done with proprietary software.

I would like to know the evidence and logic behind that claim.

> * Many microscope makers package pretty good presentation/analysis
>   software with their system, e.g. Zen for Zeiss, Elements for Nikon.  
>   This is often much more user-friendly.

At least sometimes correctness beats user-friendliness: Just the other day
I found a bug in a Wavelet implementation (instead of factors 1,4,6,4,1 it
used 1,4,6,1,1, clearly a typo). Personally, I like it when I can
investigate such a bug not having to ask whether it is possible that
there is a bug and waiting for an answer but being able to point at the
bug directly, and when the website has a corrected version the next day.

If you think that correctness in image processing is easy, have a look at
this page, and weep: http://www.4p8.com/eric.brasseur/gamma.html (Note
that I am not saying that this applies to images recorded by a confocal
microscope, but maybe you want to question the way standard software
displays those images after reading through that webpage).

Ciao,
Johannes

[Dan Metcalf]

I like ImageJ it's free and flexible once you know what you're doing.

Volocity is very good for 3D rendering and has a very user-friendly way of identifying objects and getting measurements.

You could also try Imaris.

[Daniel James White]

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Hi Venkat,

On Sep 23, 2011, at 7:02 AM, CONFOCALMICROSCOPY automatic digest system wrote:

> Date:    Thu, 22 Sep 2011 16:23:42 -0400
> From:    John Oreopoulos <[hidden email]>
>
> Try ImageJ. It's free:
>
> http://rsbweb.nih.gov/ij/

And if you like ImageJ, you should really really like Fiji,
since its just imageJ, but with a bunch of nice stuff added to make it easier to use, update and script etc.

http://fiji.sc        Fiji -  is just ImageJ (Batteries Included)

Its made by the same folks who are making ImageJ2, LOCI's Bio-formats and lots of cool plugind bundled with Fiji.
Many Fiji features already got absorbed into ImageJ, and even more will be in imagej2.

For a facility, open platforms make a lot of sense, from efficient and practical standpoints.
Also the users are given more transferable skills which they can take anywhere.
Conversely, if users are trained in a closed platform, then they are married to that,
and are in trouble when they move on and don't have a license for that software, and worse cant afford one.

That said, for Deconvolution, Huygens is very very good,
Imaris has some nice features, as do Volocity, and other expensive softwares...
but if I can train a user to do what they want
in Fiji, or cell profiler, etc.,  and later R for analysis instead of Matlab or SPSS, then thats best all round.  

I think its good to use the resources that you would otherwise spend on expensive license to hire a programmer to contribute
useful new tools to the community, as an Im,ageJ/Fiji plugin or similar.
Our facility users always want to do something special that no software can currently do easily,
and it takes years for commercial vendors to come up with the little feature you desperately need,
so its more efficient to do it yourself - and the whole community also gets the fruit of your labour
and its publishable and citeable!


cheers

Dan

>
>
> On 2011-09-22, at 11:39 AM, Ramshesh, Venkat K wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=3Dconfocalmicroscopy
>> *****
>> =20
>> Dear all,
>> =20
>> Our imaging core is looking to buy imaging software for offline image =
> processing, quantification etc. for mostly confocal and multiphoton =
> fluorescence microscopy. I was hoping if folks here had any suggestions =
> or recommendations as to which software to purchase in this regard. =
> Thanks for all your help in advance.
>> =20
>> Best,
>> Venkat
>> =20
>> Venkat Ramshesh, PhD
>> Research Instructor/Facility Manager
>> Department of Pharmaceutical and Biomedical Scinces and Hollings =
> Cancer Center
>> Drug Discovery Bldg. DD 507
>> 70 President Street, MSC 140
>> MUSC, Charleston, SC 29425
>> Ph: 8438762363
>> Fax:[phone]
>> E-mail: [hidden email]

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 )

[Nuno Moreno]

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Hi,

Don't buy. Use ImageJ.

Regards,
NM



On Sep 22, 2011, at 4:39 PM, Ramshesh, Venkat K wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Dear all,
>
> Our imaging core is looking to buy imaging software for offline image processing, quantification etc. for mostly confocal and multiphoton fluorescence microscopy. I was hoping if folks here had any suggestions or recommendations as to which software to purchase in this regard. Thanks for all your help in advance.
>
> Best,
> Venkat
>
> Venkat Ramshesh, PhD
> Research Instructor/Facility Manager
> Department of Pharmaceutical and Biomedical Scinces and Hollings Cancer Center
> Drug Discovery Bldg. DD 507
> 70 President Street, MSC 140
> MUSC, Charleston, SC 29425
> Ph: 8438762363
> Fax:[phone]
> E-mail: [hidden email]

[Vonderheit, Andreas]

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Dear Venkat,
It totally depends on what you want to do.
There are very nice open source tools around, of course if you also want to do 3D volume rendering and measuring distances or volumes, or trace neurons it is difficult to find a software capable of doing everything.
I totally do not have any commercial interest, I just recently discussed different option in image processing for a grant and I just (more less) copy and paste the information here.
The list is far from being complete, and I am happy to have learned (thanks to  Johan) about "endrov", which I did not know before.
Here it is:

We use different types of open source software.
OMERO (http://www.openmicroscopy.org/site) is our standard Image database for archiving the images and annotating and sharing them.
For simple image processing we are using Fiji (http://fiji.sc/wiki/index.php/Fiji), an ImageJ derivative, comes with a certain amount of pre-installed plug-ins.
For segmentation and quantitative measurement of phenotypes we are using CellProfiler (http://www.cellprofiler.org/).
For image analysis of time lapse movies and tracking of individual cells we are using CellCognition (http://www.cellcognition.org/).
For registration (stitching) we are using XuvTools (http://www.xuvtools.org/).

In the field of 3D and 4D visualization, rendering and measurement options following software could be used.

V3D by Hanchuan Peng http://penglab.janelia.org/proj/v3d
This software can do quite a lot, like 3D and 4D visualization, orthoslice, Neurotracing. The rendering is possible, but quite complicated to adjust, since all values have to be set before calculation, and afterwards the values cannot be changed or adjusted. The calculation of the rendering is very slow. Measurement tools are missing. Something important like an undo-button is missing. When we tested the software it crashed several times.

BioImageXD http://www.bioimagexd.net/index.php
This software can read the Leica-lif-format. The GUI looks quite similar to Imaris. Volume rendering and creation of orthoslices can be made easily; the visualization is slow and fuzzy. Right now there is no distance, area, and volume measurement tool, but this is on the list for future development. A neurotracing is also not available. This open source software is one of the better ones and as soon as the measurement tools are established a possible alternative to commercial ones.

ImageSurfer http://imagesurfer.cs.unc.edu/ 
This software is java-based and even comes with a deconvolution option. The import of image stacks is quite complicated, since no RGB-stacks are allowed and the grayscale images has to have z, time, and channel information. The supported file formats are a little outdated. Once imported, isosurfaces and volumes can be created and coloured. Orthoslices are possible. The measurement of distances between objects in the 3D volume is not possible. Also the creation of a movie while the 3D-volume is turning or orthoslices are enabled is not possible.

ImageJ or Fiji http://fiji.sc/wiki/index.php/Fiji
To visualize a three dimensional image stack one can use for instance the plug-in "ImageJ 3D Viewer", in this viewer the background can be changed and an animation can be recorded. The stack can be shown as volume or as orthoslice. Surface rendering is not possible for single channels. This plug-in is quite powerful and works nicely without crashes. Measurements are not possible.

Here some commercial software:
* Imaris from Bitplane
* Amira from Visage Imaging
* Volocity from Perkin Elmer
* Arivis browser from Arivis

Best regards
Andreas

Dr. Andreas Vonderheit
Head of Core Facility Microscopy
Core Facilities and Technology
Institute of Molecular Biology
www.imb-mainz.de
http://www.imb-mainz.de/core-facilities/microscopy/



and use OMERO for image storage
http://www.openmicroscopy.org

and why not also have a look at

http://www.endrov.net

while you are at it. open source image processing is making great strides at the moment; there is no reason to throw money at the commercial offerings. if you have money to spare, you get more for it by improving our open source software!

/Johan

------------------------------

End of CONFOCALMICROSCOPY Digest - 21 Sep 2011 to 22 Sep 2011 (#2011-34)
************************************************************************

[Hrach, Kathy]

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Dear Venkat,

Please note that this is a *commercial response* - as I represent Media Cybernetics, an imaging software organization.

All of the packages listed in this thread are quite good, and in the end, I'm sure you'll be pleased with your choice.

In addition to considering which features you'll need, you may also want to consider support/training when choosing software packages. Perhaps the most frequent feedback we receive from our software users are requests to develop more online training and "getting started" tools.  We all know it can be quite frustrating to sit staring at your monitor, not knowing what button to push first.  

For example, to help users get started with our Image-Pro Plus analysis and AutoQuant deconvolution software, we offer a number of free tutorial videos, educational webinars, and user groups. You may also want to consider if your users would need access to live training or technical support - be it via phone, email or web conferencing.  

In this era of YouTube and limited employee resources, we all want to quickly "see" how to do something and get started. Gone are the days when we can sit around studying manuals for weeks on end!

Best of luck to you,
Kathy

Kathy Hrach
Product Manager
Media Cybernetics
4340 East-West Hwy, Suite 400
Bethesda, MD 20814
Phone: [phone] ext.260
Mobile: [phone]
Email: [hidden email]
www.mediacy.com

Attend our free Imaging Webinars:
http://www.mediacy.com/index.aspx?page=WebinarCalendar 
 
Check out the Image-Pro Plus Video Library:
http://www.mediacy.com/index.aspx?page=IPPTours 

Join the Facebook Image-Pro Users Group:
http://www.facebook.com/#!/groups/44536513482/ 


On 2011-09-22, at 11:39 AM, Ramshesh, Venkat K wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Dear all,
>
> Our imaging core is looking to buy imaging software for offline image processing, quantification etc. for mostly confocal and multiphoton fluorescence microscopy. I was hoping if folks here had any suggestions or recommendations as to which software to purchase in this regard. Thanks for all your help in advance.
>
> Best,
> Venkat
>
> Venkat Ramshesh, PhD
> Research Instructor/Facility Manager
> Department of Pharmaceutical and Biomedical Scinces and Hollings Cancer Center
> Drug Discovery Bldg. DD 507
> 70 President Street, MSC 140
> MUSC, Charleston, SC 29425
> Ph: 8438762363
> Fax:[phone]
> E-mail: [hidden email]

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[Scott, Mark]

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Hi Venkat,

As many have already suggested ImageJ (or FIJI) is a very nice option since it will do almost anything you could require of it and it is free.   However, it is a rather cut down UI typical of open source software and as such isn't the most user friendly of available software - and as it is for a facility it is important that your users feel comfortable with using the software (yes it might be feasible for you and I to learn how to do something but not all microscope users are as comfortable with this thought).

Other generalised software would include Volocity and Imaris, both very nicely packaged.   There are also of course a lot of other software solutions out there designed around specific analysis problems such as Autoquant, Definiens (which is working with OMERO importation now afaik) and many others.

I guess one thing to do is assess what the users of your facility are likely to need (or currently need) and go from there.  There is little sense in buying an expensive package in for a specific purpose for only a single user when ImageJ may do it and it isn't too bad to ask one user to learn it, but likewise if a lot of users want a similar feature then it becomes more important to assess ease of use as well as cost.  No sense havign free software that is never used due to uses being scared of it.

Cheers


Mark Scott

FILM - Facility for Imaging by Light Microscopy
Senior Research Technician
Sir Alexander Fleming Building, desk 408
Imperial College London / South Kensington
Exhibition Road
London SW7 2AZ
UK
Tel: ++44(0)20-759-49793
E-mail: [hidden email]
Website: http://imperial.ac.uk/imagingfacility 



-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Ramshesh, Venkat K
Sent: 22 September 2011 16:39
To: [hidden email]
Subject: Image Processing Software

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Dear all,

Our imaging core is looking to buy imaging software for offline image processing, quantification etc. for mostly confocal and multiphoton fluorescence microscopy. I was hoping if folks here had any suggestions or recommendations as to which software to purchase in this regard. Thanks for all your help in advance.

Best,
Venkat

Venkat Ramshesh, PhD
Research Instructor/Facility Manager
Department of Pharmaceutical and Biomedical Scinces and Hollings Cancer Center
Drug Discovery Bldg. DD 507
70 President Street, MSC 140
MUSC, Charleston, SC 29425
Ph: 8438762363
Fax:[phone]
E-mail: [hidden email]

[Vincent Schoonderwoert]

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  *commercial response* Scientific Volume Imaging - makers of the
Huygens software

Dear Venkat,

To make a good choice between the list of software packages that have
already been suggested, a number of factors may be considered:

- quality of the output images (deconvolved, rendered)
- available features
- intuitive
- speed
- handling of large datasets
- hardware/OS compatibility
- type of users (beginners, advanced or both)
- pricing
- support and maintenance (manuals, trainings, webinfo like a Wiki)

Factors that seem less essential at the initial purchase but that are as
important:
- pricing of new maintenance and upgrade contracts (annual fee)
- continuity of software upgrades/updates
- quality of upgrades (new added features)

To explore the first six options, we would advise to test softwares side
by side.
To minimize the time researchers need to invest in this, some personal
advise (phone, email, remote session) may come out handy. We have
experienced that such a remote session is highly appreciated and can
give the user(s)/facility managers a quick impression of what the
software (in our case 'Huygens') can do. We mostly give sessions of
1-1.5 hours, during which all the features can be explained. Other
factors like support and upgrades can also be discussed then. We hope
our contribution will help you in your decision.


Good luck with your quest,
Vincent

***********************************************************
Vincent Schoonderwoert, PhD
Imaging Specialist/Account Manager

Scientific Volume Imaging bv
Laapersveld 63
1213 VB Hilversum, The Netherlands
Tel: + 31 35 646 8216
Fax: + 31 35 683 7971
www.svi.nl
***********************************************************




On 09/22/2011 05:39 PM, Ramshesh, Venkat K wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Dear all,
>
> Our imaging core is looking to buy imaging software for offline image processing, quantification etc. for mostly confocal and multiphoton fluorescence microscopy. I was hoping if folks here had any suggestions or recommendations as to which software to purchase in this regard. Thanks for all your help in advance.
>
> Best,
> Venkat
>
> Venkat Ramshesh, PhD
> Research Instructor/Facility Manager
> Department of Pharmaceutical and Biomedical Scinces and Hollings Cancer Center
> Drug Discovery Bldg. DD 507
> 70 President Street, MSC 140
> MUSC, Charleston, SC 29425
> Ph: 8438762363
> Fax:[phone]
> E-mail: [hidden email]
>

[Gitta Hamel]

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/  *commercial response*  Scientific Volume Imaging - makers of the Huygens software/


Dear Venkat,

To make a good choice between the list of software packages that have already been suggested, a number of factors may be considered:

- quality of the output images (deconvolved, rendered)
- available features
- intuitive
- speed
- handling of large datasets
- hardware/OS compatibility
- type of users (beginners, advanced or both)
- pricing
- support and maintenance (manuals, trainings, web-info like a Support Wiki)

Factors that seem less essential at the initial purchase but that are as important:
- pricing of new maintenance and upgrade contracts (annual fee)
- continuity of software upgrades/updates
- quality of upgrades (new added features)

To explore the first six options, we would advise to test softwares side by side.
To minimize the time researchers need to invest in this, some personal advise (phone, email, remote session) may come out handy. We have experienced that such a remote session is highly appreciated and can give the user(s)/facility managers a quick impression of what the software (in our case 'Huygens') can do. We mostly give sessions of 1-1.5 hours, during which all the Huygens features can be explained. Other factors like support and upgrades can also be discussed then. We hope our contribution will help you in your decision.


Good luck with your quest,

  On behalf of the Huygens team,

Vincent Schoonderwoert
[hidden email]

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Dear Venkat,
> It totally depends on what you want to do.
> There are very nice open source tools around, of course if you also want to do 3D volume rendering and measuring distances or volumes, or trace neurons it is difficult to find a software capable of doing everything.
> I totally do not have any commercial interest, I just recently discussed different option in image processing for a grant and I just (more less) copy and paste the information here.
> The list is far from being complete, and I am happy to have learned (thanks to  Johan) about "endrov", which I did not know before.
> Here it is:
>
> We use different types of open source software.
> OMERO (http://www.openmicroscopy.org/site) is our standard Image database for archiving the images and annotating and sharing them.
> For simple image processing we are using Fiji (http://fiji.sc/wiki/index.php/Fiji), an ImageJ derivative, comes with a certain amount of pre-installed plug-ins.
> For segmentation and quantitative measurement of phenotypes we are using CellProfiler (http://www.cellprofiler.org/).
> For image analysis of time lapse movies and tracking of individual cells we are using CellCognition (http://www.cellcognition.org/).
> For registration (stitching) we are using XuvTools (http://www.xuvtools.org/).
>
> In the field of 3D and 4D visualization, rendering and measurement options following software could be used.
>
> V3D by Hanchuan Peng http://penglab.janelia.org/proj/v3d
> This software can do quite a lot, like 3D and 4D visualization, orthoslice, Neurotracing. The rendering is possible, but quite complicated to adjust, since all values have to be set before calculation, and afterwards the values cannot be changed or adjusted. The calculation of the rendering is very slow. Measurement tools are missing. Something important like an undo-button is missing. When we tested the software it crashed several times.
>
> BioImageXD http://www.bioimagexd.net/index.php
> This software can read the Leica-lif-format. The GUI looks quite similar to Imaris. Volume rendering and creation of orthoslices can be made easily; the visualization is slow and fuzzy. Right now there is no distance, area, and volume measurement tool, but this is on the list for future development. A neurotracing is also not available. This open source software is one of the better ones and as soon as the measurement tools are established a possible alternative to commercial ones.
>
> ImageSurfer http://imagesurfer.cs.unc.edu/
> This software is java-based and even comes with a deconvolution option. The import of image stacks is quite complicated, since no RGB-stacks are allowed and the grayscale images has to have z, time, and channel information. The supported file formats are a little outdated. Once imported, isosurfaces and volumes can be created and coloured. Orthoslices are possible. The measurement of distances between objects in the 3D volume is not possible. Also the creation of a movie while the 3D-volume is turning or orthoslices are enabled is not possible.
>
> ImageJ or Fiji http://fiji.sc/wiki/index.php/Fiji
> To visualize a three dimensional image stack one can use for instance the plug-in "ImageJ 3D Viewer", in this viewer the background can be changed and an animation can be recorded. The stack can be shown as volume or as orthoslice. Surface rendering is not possible for single channels. This plug-in is quite powerful and works nicely without crashes. Measurements are not possible.
>
> Here some commercial software:
> * Imaris from Bitplane
> * Amira from Visage Imaging
> * Volocity from Perkin Elmer
> * Arivis browser from Arivis
>
> Best regards
> Andreas
>
> Dr. Andreas Vonderheit
> Head of Core Facility Microscopy
> Core Facilities and Technology
> Institute of Molecular Biology
> www.imb-mainz.de
> http://www.imb-mainz.de/core-facilities/microscopy/
>
>
>
> and use OMERO for image storage
> http://www.openmicroscopy.org
>
> and why not also have a look at
>
> http://www.endrov.net
>
> while you are at it. open source image processing is making great strides at the moment; there is no reason to throw money at the commercial offerings. if you have money to spare, you get more for it by improving our open source software!
>
> /Johan
>
> ------------------------------
>
> End of CONFOCALMICROSCOPY Digest - 21 Sep 2011 to 22 Sep 2011 (#2011-34)
> ************************************************************************
>

[Daniel James White]

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To join, leave or search the confocal microscopy listserv, go to:
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Hi Guys,

> Date:    Mon, 26 Sep 2011 12:20:32 +0000
> From:    "Scott, Mark" <[hidden email]>
> Subject: Re: Image Processing Software
>
>
> Hi Venkat,
>
> As many have already suggested ImageJ (or FIJI) is a very nice option since=
> it will do almost anything you could require of it and it is free.   Howev=
> er, it is a rather cut down UI typical of open source software

Thats a rather sweeping generalization, and possibly a little inaccurate?
There are very many open source free softwares that have very nice
extensive and feature complete user friendly graphical user interfaces.
Ever heard of the Firefox web browser? Seen Icy? Seen PyMol and VMD?

Certainly imageJ has a low complexity tool bar only primary interface,
and that is to make it less confusing and easier to use for novices.
There are not too many clickable items, so its not too scary for a new user,
but tons of functionality is there in the menus and others tools,
so in total the user interface is very very rich.

ImageJ2 project is working hard to improve the GUI,
which does have its limitations,
and the Fiji project has added many GUI/functionality enhancements like the command finder/launcher.

There is nothing to stop anyone of us making whatever GUI for imageJ2 we desire,
that will fit the needs of a certain class of users perfectly.

> and as such =
> isn't the most user friendly of available software - and as it is for a fac=
> ility it is important that your users feel comfortable with using the softw=
> are (yes it might be feasible for you and I to learn how to do something bu=
> t not all microscope users are as comfortable with this thought).

In our experience, anyone who works in a research lab is smart enough
to figure out how to use imageJ, given a bit of basic training,
and some tips and tricks, and good documentation, eg the great new  ImageJ manual,
and the websites sites of Fiji and ImageJ Documentation Wiki.

I tend to warn out users that just because an expensive software "looks" nice, doesn't mean its going to
be the best for for every job, or in fact even easy to use, once you get into the details.
Often you don't know what is really happening as the documentation is limited or missing.
Not the case for open source softwares.

Just because imageJ spits windows all over the place (which can indeed  get confusing),
doesn't necessarily put it out of reach of beginners in image processing,
in fact, because its free and open source, and easy to use,
we prefer to use Fiji for all our teaching, and as the general platform for image processing and analysis in our institute.

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 )

[Andreas Bruckbauer]

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 I find the look and feel of imageJ ok, but a serious limitation is that the image processing pipeline is not saved with the image and often there is no undo available. It is very interesting that Bitplane advertises the ImarisXT function with: "The plugin allows the exchange of 3D images between Imaris and ImageJ, thus enabling the use of the powerful image processing abilities of ImageJ on Imaris datasets".

best wishes

Andreas

 

 

-----Original Message-----
From: Daniel James White <[hidden email]>
To: CONFOCALMICROSCOPY <[hidden email]>
Sent: Tue, 27 Sep 2011 8:18
Subject: Re: Image Processing Software


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Hi Guys,



> Date:    Mon, 26 Sep 2011 12:20:32 +0000

> From:    "Scott, Mark" <[hidden email]>

> Subject: Re: Image Processing Software

>

>

> Hi Venkat,

>

> As many have already suggested ImageJ (or FIJI) is a very nice option since=

> it will do almost anything you could require of it and it is free.   Howev=

> er, it is a rather cut down UI typical of open source software



Thats a rather sweeping generalization, and possibly a little inaccurate?

There are very many open source free softwares that have very nice

extensive and feature complete user friendly graphical user interfaces.

Ever heard of the Firefox web browser? Seen Icy? Seen PyMol and VMD?



Certainly imageJ has a low complexity tool bar only primary interface,

and that is to make it less confusing and easier to use for novices.

There are not too many clickable items, so its not too scary for a new user,

but tons of functionality is there in the menus and others tools,

so in total the user interface is very very rich.



ImageJ2 project is working hard to improve the GUI,

which does have its limitations,

and the Fiji project has added many GUI/functionality enhancements like the

command finder/launcher.



There is nothing to stop anyone of us making whatever GUI for imageJ2 we desire,



that will fit the needs of a certain class of users perfectly.



> and as such =

> isn't the most user friendly of available software - and as it is for a fac=

> ility it is important that your users feel comfortable with using the softw=

> are (yes it might be feasible for you and I to learn how to do something bu=

> t not all microscope users are as comfortable with this thought).



In our experience, anyone who works in a research lab is smart enough

to figure out how to use imageJ, given a bit of basic training,

and some tips and tricks, and good documentation, eg the great new  ImageJ

manual,

and the websites sites of Fiji and ImageJ Documentation Wiki.



I tend to warn out users that just because an expensive software "looks" nice,

doesn't mean its going to

be the best for for every job, or in fact even easy to use, once you get into

the details.

Often you don't know what is really happening as the documentation is limited or

missing.

Not the case for open source softwares.



Just because imageJ spits windows all over the place (which can indeed  get

confusing),

doesn't necessarily put it out of reach of beginners in image processing,

in fact, because its free and open source, and easy to use,

we prefer to use Fiji for all our teaching, and as the general platform for

image processing and analysis in our institute.



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 )


 

[Daniel James White]

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

> Hi Andreas,
>
> On Sep 30, 2011, at 7:02 AM, CONFOCALMICROSCOPY automatic digest system wrote:
>
>> Date:    Thu, 29 Sep 2011 17:41:20 -0400
>> From:    Andreas Bruckbauer <[hidden email]>
>> Subject: Re: Image Processing Software
>>
>> I find the look and feel of imageJ ok, but a serious limitation is that th=
>> e image processing pipeline is not saved with the image and often there is =
>> no undo available.
>
> Undo is a problem, and I think the imageJ2 guys are working on that…?
>
> ...but for having a reproducible pipeline, this is not problem,
> so long as you record your commands with the macro recorder.
> Saving this as a macro is no problem…. but
> the macro is not saved in the result image….
>
> Maybe we could find a way to add the macro to the tiff header or ome metadata….
>
> We would have to listen to each image window and capture all the commands executed on it,
> and also when new image windows are generated also record how they were made…
> and probably some more fiddly cases…
>
> This might require a whole new framework, and I dont know what the
> imageJ2 guys have in mind there…regarding undo etc. #
>
>
>> It is very interesting that Bitplane advertises the Imar=
>> isXT function with: "The plugin allows the exchange of 3D images between Im=
>> aris and ImageJ, thus enabling the use of the powerful image processing abi=
>> lities of ImageJ on Imaris datasets".=20
>
> Nice eh!
>
> Dan
>
>
>>
>> best wishes
>>
>> Andreas
>

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 )

[Scott, Mark]

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Yes it was intended as a generalisation, most open source project software is slightly less robust, more buggy and lacks as nice a UI as it's more commercial counterparts.  That wasn't to say that there are exceptions to the rule and some do look nice.  Firefox isn't a realistic example though since it was designed to compete with other web-browsers of the time which clearly wasn't going to work as a legitimate competitor if it was a clunky box with pop-up windows and an unorganised UI.  

I also was not condoning other applications over ImageJ, I was simply suggesting that it is worth not discounting other commercial applications just because ImageJ is free if those commercial software package encourage users to use them more, do more work and produce results faster and easier than then having to learn ImageJ from scratch.  It seems certain members of the imaging community are rather touchy in defence of their beloved ImageJ and leap to its defence if anyone dares say anything other than that it is the only option.   I for one find that while Volocity has a nice user friendly familiar UI, it is still rather unintuitive to use, but at the same time some users much prefer this.

Using ImageJ if your users are comfortable with it is fine, but using it just out of refusing to use other applications and "forcing" users to learn ImageJ because it is what you personally like is dangerous and I was simply suggesting that all points are addressed rather than dismiss other options outright just because people who have input into ImageJ refuse to acknowledge other applications even exist.   I have seen non-computer savvy people be forced into using non-windows based platforms simply out of programmers refusing to use windows and this normally resulted in less productivity due to people not being comfortable with the other platforms.  

All I was suggesting was that there are options and opting for ImageJ because it's free or opting for other software because (as you say) it looks pretty, doesn't make it the right choice.  The end decision should come after considering the user needs and software requirements over all aspects, not just pricing and certainly not just looking nice, if it is for a multi-user facility.

Cheers
Mark


-----Original Message-----
From: Daniel James White [mailto:[hidden email]]
Sent: 27 September 2011 08:19
To: Confocal Microscopy List; Scott, Mark; [hidden email]
Subject: Re: Image Processing Software

Hi Guys,

> Date:    Mon, 26 Sep 2011 12:20:32 +0000
> From:    "Scott, Mark" <[hidden email]>
> Subject: Re: Image Processing Software
>
>
> Hi Venkat,
>
> As many have already suggested ImageJ (or FIJI) is a very nice option since=
> it will do almost anything you could require of it and it is free.   Howev=
> er, it is a rather cut down UI typical of open source software

Thats a rather sweeping generalization, and possibly a little inaccurate?
There are very many open source free softwares that have very nice
extensive and feature complete user friendly graphical user interfaces.
Ever heard of the Firefox web browser? Seen Icy? Seen PyMol and VMD?

Certainly imageJ has a low complexity tool bar only primary interface,
and that is to make it less confusing and easier to use for novices.
There are not too many clickable items, so its not too scary for a new user,
but tons of functionality is there in the menus and others tools,
so in total the user interface is very very rich.

ImageJ2 project is working hard to improve the GUI,
which does have its limitations,
and the Fiji project has added many GUI/functionality enhancements like the command finder/launcher.

There is nothing to stop anyone of us making whatever GUI for imageJ2 we desire,
that will fit the needs of a certain class of users perfectly.

> and as such =
> isn't the most user friendly of available software - and as it is for a fac=
> ility it is important that your users feel comfortable with using the softw=
> are (yes it might be feasible for you and I to learn how to do something bu=
> t not all microscope users are as comfortable with this thought).

In our experience, anyone who works in a research lab is smart enough
to figure out how to use imageJ, given a bit of basic training,
and some tips and tricks, and good documentation, eg the great new  ImageJ manual,
and the websites sites of Fiji and ImageJ Documentation Wiki.

I tend to warn out users that just because an expensive software "looks" nice, doesn't mean its going to
be the best for for every job, or in fact even easy to use, once you get into the details.
Often you don't know what is really happening as the documentation is limited or missing.
Not the case for open source softwares.

Just because imageJ spits windows all over the place (which can indeed  get confusing),
doesn't necessarily put it out of reach of beginners in image processing,
in fact, because its free and open source, and easy to use,
we prefer to use Fiji for all our teaching, and as the general platform for image processing and analysis in our institute.

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 )

[Daniel James White]

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

Hi Mark,

On Sep 30, 2011, at 12:38 PM, Scott, Mark wrote:

> Yes it was intended as a generalisation, most open source project software is slightly less robust, more buggy and lacks as nice a UI as it's more commercial counterparts.

Do you have objective data to back that statement up, or is it just your feeling or experience?
I think it does a diservice to the many well maintained, well designed, stable and user friendly open source softwares that are used in our discipline and many others.

Sure, there is crap open source software too, but there are also very poor expensive softwares and also very good ones.

My objection is the labeling of open source software with an automatic lower quality than commercial software.
This isn't really fair, and each case should be made on its own merits.

> That wasn't to say that there are exceptions to the rule

What rule? Where is the data to prove any such rule?

> and some do look nice.  Firefox isn't a realistic example though since it was designed to compete with other web-browsers of the time which clearly wasn't going to work as a legitimate competitor if it was a clunky box with pop-up windows and an unorganised UI.  
>
> I also was not condoning other applications over ImageJ, I was simply suggesting that it is worth not discounting other commercial applications just because ImageJ is free if those commercial software package encourage users to use them more, do more work and produce results faster and easier than then having to learn ImageJ from scratch.  

|I totally agree.
However, the big picture view, in my experience, is that the "Ease of use and fast results, / no need to develop your own tools" draw of commercial software is often an illusion. There are very strong cases where commercial software is very very good at a certain thiung.. eg  Huygens for deconvolution. But if you dont happen to hit one of those specific applications and you need something just a little or very different, an open software platform where you can chain together existing tools and add your own special little bits pays off big time.

ImarisXT is a good thing as it enhances a closed platform by leveraging an open one! Smart!

> It seems certain members of the imaging community are rather touchy in defence of their beloved ImageJ and leap to its defence if anyone dares say anything other than that it is the only option.

Did anyone say its the only option? Certainly many folks think it's avery good option. But commercial software can also be a good fit if it really does exactly what you want already. Beware the specter of "vendor lock-in" though......
Give a man a fish and he can eat for one day. Teach a man to fish and he can feed his family for a lifetime.  

>   I for one find that while Volocity has a nice user friendly familiar UI, it is still rather unintuitive to use, but at the same time some users much prefer this.

Every human is different. Some people are narrow minded and just want a "working " solution now.
Others are smarter and understand the value of open platforms being very compatible with doing good science,
and are not interested in how pretty a software looks, but rather in what it can do with not too much effort.
>
> Using ImageJ if your users are comfortable with it is fine, but using it just out of refusing to use other applications and "forcing" users to learn ImageJ because it is what you personally like is dangerous and I was simply suggesting that all points are addressed rather than dismiss other options outright just because people who have input into ImageJ refuse to acknowledge other applications even exist.  

I think I just suggested this is not the case. There is room for open source and proprietary software in this ecosystem.

>  I have seen non-computer savvy people be forced into using non-windows based platforms simply out of programmers refusing to use windows and this normally resulted in less productivity due to people not being comfortable with the other platforms.  

Perhaps in the short term, with short attention spans, this can be the case.
In the long run, investing in open platforms does pay off.
There are plenty of good reasons to use windows, but there are also some very good reasons that
the folk setting up facilities and providing infrastructure avoid it at nearly all costs... these guys are looking at the big picture.

Vendors might provide a certain closed platform or operating system on the computers attached to their microscopes,  believing that this is what most users are familiar and comfortable with.
You can ask any user of an Applied Precision DeltaVision microscope system if this actually matters.
I think its a false assumptions. Users like what works and don't care about the computer Operating System very much.

As a systems admin I very much like the Linux based systems over the window systems, as the latter provide a much more troublesome environment to keep in good shape, easily administered,  and virus free etc.

> All I was suggesting was that there are options and opting for ImageJ because it's free or opting for other software because (as you say) it looks pretty, doesn't make it the right choice.  The end decision should come after considering the user needs and software requirements over all aspects, not just pricing and certainly not just looking nice, if it is for a multi-user facility.

Absolutely right!
I think we agree on much more than you might have thought!

cheers

Dan

>
> Cheers
> Mark
>
>
> -----Original Message-----
> From: Daniel James White [mailto:[hidden email]]
> Sent: 27 September 2011 08:19
> To: Confocal Microscopy List; Scott, Mark; [hidden email]
> Subject: Re: Image Processing Software
>
> Hi Guys,
>
>> Date:    Mon, 26 Sep 2011 12:20:32 +0000
>> From:    "Scott, Mark" <[hidden email]>
>> Subject: Re: Image Processing Software
>>
>>
>> Hi Venkat,
>>
>> As many have already suggested ImageJ (or FIJI) is a very nice option since=
>> it will do almost anything you could require of it and it is free.   Howev=
>> er, it is a rather cut down UI typical of open source software
>
> Thats a rather sweeping generalization, and possibly a little inaccurate?
> There are very many open source free softwares that have very nice
> extensive and feature complete user friendly graphical user interfaces.
> Ever heard of the Firefox web browser? Seen Icy? Seen PyMol and VMD?
>
> Certainly imageJ has a low complexity tool bar only primary interface,
> and that is to make it less confusing and easier to use for novices.
> There are not too many clickable items, so its not too scary for a new user,
> but tons of functionality is there in the menus and others tools,
> so in total the user interface is very very rich.
>
> ImageJ2 project is working hard to improve the GUI,
> which does have its limitations,
> and the Fiji project has added many GUI/functionality enhancements like the command finder/launcher.
>
> There is nothing to stop anyone of us making whatever GUI for imageJ2 we desire,
> that will fit the needs of a certain class of users perfectly.
>
>> and as such =
>> isn't the most user friendly of available software - and as it is for a fac=
>> ility it is important that your users feel comfortable with using the softw=
>> are (yes it might be feasible for you and I to learn how to do something bu=
>> t not all microscope users are as comfortable with this thought).
>
> In our experience, anyone who works in a research lab is smart enough
> to figure out how to use imageJ, given a bit of basic training,
> and some tips and tricks, and good documentation, eg the great new  ImageJ manual,
> and the websites sites of Fiji and ImageJ Documentation Wiki.
>
> I tend to warn out users that just because an expensive software "looks" nice, doesn't mean its going to
> be the best for for every job, or in fact even easy to use, once you get into the details.
> Often you don't know what is really happening as the documentation is limited or missing.
> Not the case for open source softwares.
>
> Just because imageJ spits windows all over the place (which can indeed  get confusing),
> doesn't necessarily put it out of reach of beginners in image processing,
> in fact, because its free and open source, and easy to use,
> we prefer to use Fiji for all our teaching, and as the general platform for image processing and analysis in our institute.
>
> 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 )
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>

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 )