Light Lab by Carl Zeiss Microscopy for iOS devices

[Johannes Amon]

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

Dear Community,

just to inform you, we at Carl Zeiss Microscopy just recently launched a
fluorescence microscopy app for your iPads, iPhones and iPod touch devices. I
was already in contact with George McNamara as the app uses the pubspectra
database, similar to our ZEN Smart Setup, and he suggested to post it here so
that you are able to have a test-drive and discuss what you like or what you
might not like. We are completely open for ideas, so hit the inbox micro-
[hidden email], hit me, and of course also feel free to discuss the app here.

http://www.zeiss.com/micro-apps

The website should give you a good impression about what the app is able to
do. We are really curious to learn how it will be received by the scientific
community so I'll try to check back regularly and see what you think.

Have a nice weekend!

Carl Zeiss MicroImaging GmbH
Business Unit BioSciences
Imaging Software Munich

Dr. Johannes Amon
[hidden email]

[Xiang Hao]

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

Sounds great!
Do you have the plan to further "push" this project. such as transplanting this
software to Android platform?

Hao, Xiang
---
State Key Laboratory of Modern Optical Instrumentation
Zhejiang University, China

[Tim Feinstein-2]

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

Nicely done and well presented.  I like the implementation of the spectra viewer.  It has some odd missing spectra (Venus/YFP, dTomato) but I assume that can be fixed.  

No doubt you already know how much demand there is for an iOS/Android data viewer app.  I fully understand how challenging that might be, but I imagine that the vast wealth of tele-radiology solutions already out there could provide a useful template.  Maybe one of them could be jerry-rigged to work as-is…

I hope that this inspires Nikon, Leica and Olympus to answer this with applications of their own.

cheers,


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 Jan 13, 2012, at 10:26 AM, Johannes Amon wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Dear Community,
>
> just to inform you, we at Carl Zeiss Microscopy just recently launched a
> fluorescence microscopy app for your iPads, iPhones and iPod touch devices. I
> was already in contact with George McNamara as the app uses the pubspectra
> database, similar to our ZEN Smart Setup, and he suggested to post it here so
> that you are able to have a test-drive and discuss what you like or what you
> might not like. We are completely open for ideas, so hit the inbox micro-
> [hidden email], hit me, and of course also feel free to discuss the app here.
>
> http://www.zeiss.com/micro-apps
>
> The website should give you a good impression about what the app is able to
> do. We are really curious to learn how it will be received by the scientific
> community so I'll try to check back regularly and see what you think.
>
> Have a nice weekend!
>
> Carl Zeiss MicroImaging GmbH
> Business Unit BioSciences
> Imaging Software Munich
>
> Dr. Johannes Amon
> [hidden email]

[Loralei Dewe-3]

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

I too would prefer it in an Android format. I find the Android to be more
useful to me than the Apple types...

Loralei Dewe

On Fri, Jan 13, 2012 at 7:26 AM, Johannes Amon <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Dear Community,
>
> just to inform you, we at Carl Zeiss Microscopy just recently launched a
> fluorescence microscopy app for your iPads, iPhones and iPod touch
> devices. I
> was already in contact with George McNamara as the app uses the pubspectra
> database, similar to our ZEN Smart Setup, and he suggested to post it here
> so
> that you are able to have a test-drive and discuss what you like or what
> you
> might not like. We are completely open for ideas, so hit the inbox micro-
> [hidden email], hit me, and of course also feel free to discuss the app
> here.
>
> http://www.zeiss.com/micro-apps
>
> The website should give you a good impression about what the app is able to
> do. We are really curious to learn how it will be received by the
> scientific
> community so I'll try to check back regularly and see what you think.
>
> Have a nice weekend!
>
> Carl Zeiss MicroImaging GmbH
> Business Unit BioSciences
> Imaging Software Munich
>
> Dr. Johannes Amon
> [hidden email]
>

[Gabriel Lapointe-2]

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

Great news,
I can't wait to try the Android version.

Sincerely,

logo
Gabriel Lapointe, M.Sc.
[hidden email]
http://gabriellapointe.ca
logo


On Fri, 2012-01-13 at 08:55 -0800, Loralei Dewe wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> I too would prefer it in an Android format. I find the Android to be more
> useful to me than the Apple types...
>
> Loralei Dewe
>
> On Fri, Jan 13, 2012 at 7:26 AM, Johannes Amon <[hidden email]> wrote:
>
> > *****
> > To join, leave or search the confocal microscopy listserv, go to:
> > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> > *****
> >
> > Dear Community,
> >
> > just to inform you, we at Carl Zeiss Microscopy just recently launched a
> > fluorescence microscopy app for your iPads, iPhones and iPod touch
> > devices. I
> > was already in contact with George McNamara as the app uses the pubspectra
> > database, similar to our ZEN Smart Setup, and he suggested to post it here
> > so
> > that you are able to have a test-drive and discuss what you like or what
> > you
> > might not like. We are completely open for ideas, so hit the inbox micro-
> > [hidden email], hit me, and of course also feel free to discuss the app
> > here.
> >
> > http://www.zeiss.com/micro-apps
> >
> > The website should give you a good impression about what the app is able to
> > do. We are really curious to learn how it will be received by the
> > scientific
> > community so I'll try to check back regularly and see what you think.
> >
> > Have a nice weekend!
> >
> > Carl Zeiss MicroImaging GmbH
> > Business Unit BioSciences
> > Imaging Software Munich
> >
> > Dr. Johannes Amon
> > [hidden email]
> >

[Johannes Amon]

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

of course I can't tell you any specifics but at the moment we are evaluating a native port to
android ICS 4.0. at the end it always comes down to budget so it would help immensely if
you'd order some confocals right now ^^

just joking, gonna keep you posted on this project

[Peter Gabriel Pitrone]

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

I must say that I like the idea!

However, I think that this would be better if Open Microscopy Environment
would make a Smart Phone viewer so you wouldn't be limited by what
microscope system you acquired the data from to be able to see it.

What I think is that the vendors really need to focus on right now is
compatibility, but I know that they think it is "Anathema".

My $0.02 worth,

Pete

On Fri, January 13, 2012 4:26 pm, Johannes Amon wrote:
| *****
| To join, leave or search the confocal microscopy listserv, go to:
| http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
| *****
|
| Dear Community,
|
| just to inform you, we at Carl Zeiss Microscopy just recently launched a
| fluorescence microscopy app for your iPads, iPhones and iPod touch
| devices. I
| was already in contact with George McNamara as the app uses the pubspectra
| database, similar to our ZEN Smart Setup, and he suggested to post it here
| so
| that you are able to have a test-drive and discuss what you like or what
| you
| might not like. We are completely open for ideas, so hit the inbox micro-
| [hidden email], hit me, and of course also feel free to discuss the app
| here.
|
| http://www.zeiss.com/micro-apps
|
| The website should give you a good impression about what the app is able
| to
| do. We are really curious to learn how it will be received by the
| scientific
| community so I'll try to check back regularly and see what you think.
|
| Have a nice weekend!
|
| Carl Zeiss MicroImaging GmbH
| Business Unit BioSciences
| Imaging Software Munich
|
| Dr. Johannes Amon
| [hidden email]
|


--
Peter Gabriel Pitrone - TechRMS
Microscopy/Imaging Specialist
Prof. Dr. Pavel Tomancak group
Max Planck Institute for
Molecular Biology and Genetics
Pfotenhauerstr. 108
01307 Dresden

"If a straight line fit is required, obtain only two data points." - Anon.

[George McNamara]

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

Hi Pete,

I would match your $0.02 except that PubSpectra is open data access:
freely available to you, Zeiss - it has been the source of the spectral
Smart Setup in ZEN for years - and other vendors. Many vendors have
contributed data, including LfieTech/Invitrogen/Molecular Probes,
Chroma, Omega and Semrock, as have academics, including Roger
Tsien/Robert Campbell, Jonathan Lindsey (see his photochemcad site). I
have told many vendors about the data and encouraged them to include the
data in their software. I congratulate Zeiss on their introduction of
their iZeiss apps (I personally an not an i kind of guy).

The PubSpectra data set can be downloaded in the ZIP file at the top of
http://sylvester.org/shared-resources/analytical-imaging/links-forms-documentation/pubspectra-data

and the UA graphing site is http://www.spectra.arizona.edu/ - along with
additional spectra that Urs Utzinger and Carl Boswell have entered. Type
in    2p   in the dye field for data at the UA site that is not
currently in PubSpectra. Data from the UA site can even be downloaded.

I'll go further an encourage OME, ImageJ / ImageJ2 / Fiji / MBF ImageJ,
and other imaging developers, to make use of PubSpectra.

Finally, I encourage everyone who has fluorescence and fluorescence
related spectra (including, but limited to dyes, fluorescent proteins,
filters, light sources), to send me data to add to PubSpectra -
preferably in the same organization as is in the PubSpectra Excel 2007
(xlsx) file.


George


On 1/14/2012 7:18 AM, Peter Gabriel Pitrone wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> I must say that I like the idea!
>
> However, I think that this would be better if Open Microscopy Environment
> would make a Smart Phone viewer so you wouldn't be limited by what
> microscope system you acquired the data from to be able to see it.
>
> What I think is that the vendors really need to focus on right now is
> compatibility, but I know that they think it is "Anathema".
>
> My $0.02 worth,
>
> Pete
>
> On Fri, January 13, 2012 4:26 pm, Johannes Amon wrote:
> | *****
> | To join, leave or search the confocal microscopy listserv, go to:
> | http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> | *****
> |
> | Dear Community,
> |
> | just to inform you, we at Carl Zeiss Microscopy just recently launched a
> | fluorescence microscopy app for your iPads, iPhones and iPod touch
> | devices. I
> | was already in contact with George McNamara as the app uses the pubspectra
> | database, similar to our ZEN Smart Setup, and he suggested to post it here
> | so
> | that you are able to have a test-drive and discuss what you like or what
> | you
> | might not like. We are completely open for ideas, so hit the inbox micro-
> | [hidden email], hit me, and of course also feel free to discuss the app
> | here.
> |
> | http://www.zeiss.com/micro-apps
> |
> | The website should give you a good impression about what the app is able
> | to
> | do. We are really curious to learn how it will be received by the
> | scientific
> | community so I'll try to check back regularly and see what you think.
> |
> | Have a nice weekend!
> |
> | Carl Zeiss MicroImaging GmbH
> | Business Unit BioSciences
> | Imaging Software Munich
> |
> | Dr. Johannes Amon
> | [hidden email]
> |
>
>
>    

--


George McNamara, PhD
Analytical Imaging Core Facility
University of Miami

[Jason Swedlow-2]

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

Hi Pete-

Thanks for the suggestion.  Given our commitment to open source software,
it's unlikely you'll see an iOS App from OME.  You can look around the
web-- there are lots of opinions, but it's pretty clear that the GPL
license conflicts with Apple's distribution mechanisms.

We have definitely experimented with clients for mobile browsers (for devs
only,
http://trac.openmicroscopy.org.uk/ome/browser/ome.git/components/tools/OmeroWeb/omeroweb),
but this needs more work to be fully developed.  As you might imagine,
chasing all the different browser platforms and versions is just too much
fun.

Android?  Hmmmm.  In general we prefer cross-platform solutions, but the
world is changing rapidly.....

if you feel strongly about this, post it on the OME Forums (
http://www.openmicroscopy.org/community/) -- your feedback drives our
priorities.

Cheers,

Jason


On Sat, Jan 14, 2012 at 12:18 PM, Peter Gabriel Pitrone
<[hidden email]>wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> I must say that I like the idea!
>
> However, I think that this would be better if Open Microscopy Environment
> would make a Smart Phone viewer so you wouldn't be limited by what
> microscope system you acquired the data from to be able to see it.
>
> What I think is that the vendors really need to focus on right now is
> compatibility, but I know that they think it is "Anathema".
>
> My $0.02 worth,
>
> Pete
>
> On Fri, January 13, 2012 4:26 pm, Johannes Amon wrote:
> | *****
> | To join, leave or search the confocal microscopy listserv, go to:
> | http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> | *****
> |
> | Dear Community,
> |
> | just to inform you, we at Carl Zeiss Microscopy just recently launched a
> | fluorescence microscopy app for your iPads, iPhones and iPod touch
> | devices. I
> | was already in contact with George McNamara as the app uses the
> pubspectra
> | database, similar to our ZEN Smart Setup, and he suggested to post it
> here
> | so
> | that you are able to have a test-drive and discuss what you like or what
> | you
> | might not like. We are completely open for ideas, so hit the inbox micro-
> | [hidden email], hit me, and of course also feel free to discuss the app
> | here.
> |
> | http://www.zeiss.com/micro-apps
> |
> | The website should give you a good impression about what the app is able
> | to
> | do. We are really curious to learn how it will be received by the
> | scientific
> | community so I'll try to check back regularly and see what you think.
> |
> | Have a nice weekend!
> |
> | Carl Zeiss MicroImaging GmbH
> | Business Unit BioSciences
> | Imaging Software Munich
> |
> | Dr. Johannes Amon
> | [hidden email]
> |
>
>
> --
> Peter Gabriel Pitrone - TechRMS
> Microscopy/Imaging Specialist
> Prof. Dr. Pavel Tomancak group
> Max Planck Institute for
> Molecular Biology and Genetics
> Pfotenhauerstr. 108
> 01307 Dresden
>
> "If a straight line fit is required, obtain only two data points." - Anon.
>

--
**************************
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee  DD1 5EH
United Kingdom

phone [phone]
Intl phone:  [phone]
FAX   [phone]
email: [hidden email]

Lab Page: http://www.lifesci.dundee.ac.uk/gre/staff/jason-swedlow
Open Microscopy Environment: http://openmicroscopy.org
**************************

[Jason Swedlow-2]

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

Hi-

A few comments:

George's PubSpectra resource is very nice.  The usage and contributions are
exactly the kind of thing that can develop using open, shareable,
maintained resources.  I emphasise 'maintained' as anything like this must
be kept up-to-date for it to be at all useful.  George has done a great job
with it.

In OME, we provide many mechanism for storing data.  In fact, in our first
version of OME-XML, we imagined mechanisms for storing fluorescence
spectra.  As soon as we saw George's work, we were sooo happy that someone
else had taken this on, we presumed that a  URL linking to PubSpectra would
provide the simplest, most flexible mechanism for storing spectral
information.  We haven't directly specified this, as we prefer to let users
make these choices-- but we can.  In our current work, we are moving OMERO
to a stable platform in order to focus on delivering more functionality in
the clients (only if you really care,
http://trac.openmicroscopy.org.uk/ome/milestone/OMERO-Beta4.4).  Views of
PubSpectra data could certainly be implemented in the future.

As always, comments, suggestions, and biting critiques are welcome at
http://www.openmicroscopy.org/community/

And....hats off to Zeiss.  Very nice app!!!

Cheers,

Jason


On Sat, Jan 14, 2012 at 4:26 PM, George McNamara
<[hidden email]>wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/**wa?A0=confocalmicroscopy<http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>
> *****
>
> Hi Pete,
>
> I would match your $0.02 except that PubSpectra is open data access:
> freely available to you, Zeiss - it has been the source of the spectral
> Smart Setup in ZEN for years - and other vendors. Many vendors have
> contributed data, including LfieTech/Invitrogen/Molecular Probes, Chroma,
> Omega and Semrock, as have academics, including Roger Tsien/Robert
> Campbell, Jonathan Lindsey (see his photochemcad site). I have told many
> vendors about the data and encouraged them to include the data in their
> software. I congratulate Zeiss on their introduction of their iZeiss apps
> (I personally an not an i kind of guy).
>
> The PubSpectra data set can be downloaded in the ZIP file at the top of
> http://sylvester.org/shared-**resources/analytical-imaging/**
> links-forms-documentation/**pubspectra-data<http://sylvester.org/shared-resources/analytical-imaging/links-forms-documentation/pubspectra-data>
>
> and the UA graphing site is http://www.spectra.arizona.**edu/<http://www.spectra.arizona.edu/>- along with additional spectra that Urs Utzinger and Carl Boswell have
> entered. Type in    2p   in the dye field for data at the UA site that is
> not currently in PubSpectra. Data from the UA site can even be downloaded.
>
> I'll go further an encourage OME, ImageJ / ImageJ2 / Fiji / MBF ImageJ,
> and other imaging developers, to make use of PubSpectra.
>
> Finally, I encourage everyone who has fluorescence and fluorescence
> related spectra (including, but limited to dyes, fluorescent proteins,
> filters, light sources), to send me data to add to PubSpectra - preferably
> in the same organization as is in the PubSpectra Excel 2007 (xlsx) file.
>
>
> George
>
>
> On 1/14/2012 7:18 AM, Peter Gabriel Pitrone wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/**wa?A0=confocalmicroscopy<http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>
>> *****
>>
>> I must say that I like the idea!
>>
>> However, I think that this would be better if Open Microscopy Environment
>> would make a Smart Phone viewer so you wouldn't be limited by what
>> microscope system you acquired the data from to be able to see it.
>>
>> What I think is that the vendors really need to focus on right now is
>> compatibility, but I know that they think it is "Anathema".
>>
>> My $0.02 worth,
>>
>> Pete
>>
>> On Fri, January 13, 2012 4:26 pm, Johannes Amon wrote:
>> | *****
>> | To join, leave or search the confocal microscopy listserv, go to:
>> | http://lists.umn.edu/cgi-bin/**wa?A0=confocalmicroscopy<http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>
>> | *****
>> |
>> | Dear Community,
>> |
>> | just to inform you, we at Carl Zeiss Microscopy just recently launched a
>> | fluorescence microscopy app for your iPads, iPhones and iPod touch
>> | devices. I
>> | was already in contact with George McNamara as the app uses the
>> pubspectra
>> | database, similar to our ZEN Smart Setup, and he suggested to post it
>> here
>> | so
>> | that you are able to have a test-drive and discuss what you like or what
>> | you
>> | might not like. We are completely open for ideas, so hit the inbox
>> micro-
>> | [hidden email], hit me, and of course also feel free to discuss the app
>> | here.
>> |
>> | http://www.zeiss.com/micro-**apps <http://www.zeiss.com/micro-apps>
>> |
>> | The website should give you a good impression about what the app is able
>> | to
>> | do. We are really curious to learn how it will be received by the
>> | scientific
>> | community so I'll try to check back regularly and see what you think.
>> |
>> | Have a nice weekend!
>> |
>> | Carl Zeiss MicroImaging GmbH
>> | Business Unit BioSciences
>> | Imaging Software Munich
>> |
>> | Dr. Johannes Amon
>> | [hidden email]
>> |
>>
>>
>>
>>
>
>
> --
>
>
> George McNamara, PhD
> Analytical Imaging Core Facility
> University of Miami
>

--
**************************
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee  DD1 5EH
United Kingdom

phone [phone]
Intl phone:  [phone]
FAX   [phone]
email: [hidden email]

Lab Page: http://www.lifesci.dundee.ac.uk/gre/staff/jason-swedlow
Open Microscopy Environment: http://openmicroscopy.org
**************************

[Michael Herron]

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

PubSpectra needs Flash so it does not work on iPhone or iPad. Any plans to
make it HTML5 compliant?

On Saturday, January 14, 2012, Jason Swedlow <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi-
>
> A few comments:
>
> George's PubSpectra resource is very nice.  The usage and contributions

are
> exactly the kind of thing that can develop using open, shareable,
> maintained resources.  I emphasise 'maintained' as anything like this must
> be kept up-to-date for it to be at all useful.  George has done a great
job
> with it.
>
> In OME, we provide many mechanism for storing data.  In fact, in our first
> version of OME-XML, we imagined mechanisms for storing fluorescence
> spectra.  As soon as we saw George's work, we were sooo happy that someone
> else had taken this on, we presumed that a  URL linking to PubSpectra
would
> provide the simplest, most flexible mechanism for storing spectral
> information.  We haven't directly specified this, as we prefer to let
users

> make these choices-- but we can.  In our current work, we are moving OMERO
> to a stable platform in order to focus on delivering more functionality in
> the clients (only if you really care,
> http://trac.openmicroscopy.org.uk/ome/milestone/OMERO-Beta4.4).  Views of
> PubSpectra data could certainly be implemented in the future.
>
> As always, comments, suggestions, and biting critiques are welcome at
> http://www.openmicroscopy.org/community/
>
> And....hats off to Zeiss.  Very nice app!!!
>
> Cheers,
>
> Jason
>
>
> On Sat, Jan 14, 2012 at 4:26 PM, George McNamara
> <[hidden email]>wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/**wa?A0=confocalmicroscopy<

http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>

>> *****
>>
>> Hi Pete,
>>
>> I would match your $0.02 except that PubSpectra is open data access:
>> freely available to you, Zeiss - it has been the source of the spectral
>> Smart Setup in ZEN for years - and other vendors. Many vendors have
>> contributed data, including LfieTech/Invitrogen/Molecular Probes, Chroma,
>> Omega and Semrock, as have academics, including Roger Tsien/Robert
>> Campbell, Jonathan Lindsey (see his photochemcad site). I have told many
>> vendors about the data and encouraged them to include the data in their
>> software. I congratulate Zeiss on their introduction of their iZeiss apps
>> (I personally an not an i kind of guy).
>>
>> The PubSpectra data set can be downloaded in the ZIP file at the top of
>> http://sylvester.org/shared-**resources/analytical-imaging/**
>> links-forms-documentation/**pubspectra-data<

http://sylvester.org/shared-resources/analytical-imaging/links-forms-documentation/pubspectra-data
>
>>
>> and the UA graphing site is http://www.spectra.arizona.**edu/<
http://www.spectra.arizona.edu/>- along with additional spectra that Urs
Utzinger and Carl Boswell have
>> entered. Type in    2p   in the dye field for data at the UA site that is
>> not currently in PubSpectra. Data from the UA site can even be
downloaded.
>>
>> I'll go further an encourage OME, ImageJ / ImageJ2 / Fiji / MBF ImageJ,
>> and other imaging developers, to make use of PubSpectra.
>>
>> Finally, I encourage everyone who has fluorescence and fluorescence
>> related spectra (including, but limited to dyes, fluorescent proteins,
>> filters, light sources), to send me data to add to PubSpectra -
preferably

>> in the same organization as is in the PubSpectra Excel 2007 (xlsx) file.
>>
>>
>> George
>>
>>
>> On 1/14/2012 7:18 AM, Peter Gabriel Pitrone wrote:
>>
>>> *****
>>> To join, leave or search the confocal microscopy listserv, go to:
>>> http://lists.umn.edu/cgi-bin/**wa?A0=confocalmicroscopy<

http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>
>>> *****
>>>
>>> I must say that I like the idea!
>>>
>>> However, I think that this would be better if Open Microscopy
Environment

>>> would make a Smart Phone viewer so you wouldn't be limited by what
>>> microscope system you acquired the data from to be able to see it.
>>>
>>> What I think is that the vendors really need to focus on right now is
>>> compatibility, but I know that they think it is "Anathema".
>>>
>>> My $0.02 worth,
>>>
>>> Pete
>>>
>>> On Fri, January 13, 2012 4:26 pm, Johannes Amon wrote:
>>> | *****
>>> | To join, leave or search the confocal microscopy listserv, go to:
>>> | http://lists.umn.edu/cgi-bin/**wa?A0=confocalmicroscopy<

http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>
>>> | *****
>>> |
>>> | Dear Community,
>>> |
>>> | just to inform you, we at Carl Zeiss Microscopy just recently
launched a
>>> | fluorescence microscopy app for your iPads, iPhones and iPod touch
>>> | devices. I
>>> | was already in contact with George McNamara as the app uses the
>>> pubspectra
>>> | database, similar to our ZEN Smart Setup, and he suggested to post it
>>> here
>>> | so
>>> | that you are able to have a test-drive and discuss what you like or
what
>>> | you
>>> | might not like. We are completely open for ideas, so hit the inbox
>>> micro-
>>> | [hidden email], hit me, and of course also feel free to discuss the app
>>> | here.
>>> |
>>> | http://www.zeiss.com/micro-**apps <http://www.zeiss.com/micro-apps>
>>> |
>>> | The website should give you a good impression about what the app is
able

>>> | to
>>> | do. We are really curious to learn how it will be received by the
>>> | scientific
>>> | community so I'll try to check back regularly and see what you think.
>>> |
>>> | Have a nice weekend!
>>> |
>>> | Carl Zeiss MicroImaging GmbH
>>> | Business Unit BioSciences
>>> | Imaging Software Munich
>>> |
>>> | Dr. Johannes Amon
>>> | [hidden email]
>>> |
>>>
>>>
>>>
>>>
>>
>>
>> --
>>
>>
>> George McNamara, PhD
>> Analytical Imaging Core Facility
>> University of Miami
>>
>
>
>
> --
> **************************
> Wellcome Trust Centre for Gene Regulation & Expression
> College of Life Sciences
> MSI/WTB/JBC Complex
> University of Dundee
> Dow Street
> Dundee  DD1 5EH
> United Kingdom
>
> phone [phone]
> Intl phone:  [phone]
> FAX   [phone]
> email: [hidden email]
>
> Lab Page: http://www.lifesci.dundee.ac.uk/gre/staff/jason-swedlow
> Open Microscopy Environment: http://openmicroscopy.org
> **************************
>

--
Michael J. Herron,  U of MN, Dept. of Entomology
  [hidden email]
     612-624-3688 (office) 612-625-5299 (FAX)

[George McNamara]

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

Hi Michael,

PubSpectra is the open data access project - that is, the Excel file
that everyone can freely use. The xlsx file format is XML, though
Internet Explorer 8 in Windows takes the lazy way out by simply
launching Excel. Perhaps Android and/or iThingies have Excel or useful
Excel viewers. My limited experience a couple of years ago with the
spreadsheet program in Open Office (for Windows) was that it was lame.

You are probably referring to Urs Utzinger's Spectra Database hosted at
the University of Arizona, http://www.spectra.arizona.edu/     -
non-Flash version(s) are for Urs to respond to.

***

I want to encourage everyone to make your data available as Open Data.
There are some guidelines:

http://pantonprinciples.org/


            Science is based on building on, reusing and openly
            criticising the published body of scientific knowledge.


            For science to effectively function, and for society to reap
            the full benefits from scientific endeavours, it is crucial
            that science data be made open <http://opendefinition.org/>.

        By open data in science we mean that it is freely available on
        the public internet permitting any user to download, copy,
        analyse, re-process, pass them to software or use them for any
        other purpose without financial, legal, or technical barriers
        other than those inseparable from gaining access to the internet
        itself. *To this end data related to published science should be
        explicitly placed in the public domain.*

        *Formally, we recommend adopting and acting on the following
        principles:*

           1.

              Where data or collections of data are published it is
              critical that they be published with a clear and explicit
              statement of the wishes and expectations of the publishers
              with respect to re-use and re-purposing of individual data
              elements, the whole data collection, and subsets of the
              collection. This statement should be precise, irrevocable,
              and based on an appropriate and recognized legal statement
              in the form of a waiver or license.

              /When publishing data make an explicit and robust
              statement of your wishes./

           2.

              Many widely recognized licenses are not intended for, and
              are not appropriate for, data or collections of data. A
              variety of waivers and licenses that are designed for and
              appropriate for the treatment of data are described here
              <http://opendefinition.org/licenses#Data>. Creative
              Commons licenses (apart from CCZero), GFDL, GPL, BSD, etc
              are NOT appropriate for data and their use is STRONGLY
              discouraged.

              /Use a recognized waiver or license that is appropriate
              for data./

           3.

              The use of licenses which limit commercial re-use or limit
              the production of derivative works by excluding use for
              particular purposes or by specific persons or
              organizations is STRONGLY discouraged. These licenses make
              it impossible to effectively integrate and re-purpose
              datasets and prevent commercial activities that could be
              used to support data preservation.

              /If you want your data to be effectively used and added to
              by others it should be open as defined by the Open
              Knowledge/Data Definition <http://opendefinition.org/> --
              in particular non-commercial and other restrictive clauses
              should not be used./

           4.

              Furthermore, in science it is STRONGLY recommended that
              data, especially where publicly funded, be explicitly
              placed in the public domain via the use of the Public
              Domain Dedication and Licence or Creative Commons Zero
              Waiver. This is in keeping with the public funding of much
              scientific research and the general ethos of sharing and
              re-use within the scientific community.

              /Explicit dedication of data underlying published science
              into the public domain via PDDL or CCZero is strongly
              recommended and ensures compliance with both the Science
              Commons Protocol for Implementing Open Access Data
              <http://sciencecommons.org/projects/publishing/open-access-data-protocol/>
              and the Open Knowledge/Data Definition
              <http://opendefinition.org/>./

See also http://www.arl.org/sparc/opendata/  and
http://www.arl.org/sparc/innovator/panton.shtml  - in particular the
latter explains the Panton in Panton Principles.

I've already stated my position (2006 Cytometry paper on PubSpectra and
Carl Boswell's first generation UA Graphing site (
http://www.mcb.arizona.edu/ipc/fret/index.html -- which is still
available ):

        "... data is not subject to copyright. Text and commentary about
        Feist (Feist Publications, Inc. v. Rural Tel. Serv. Co. 1991;499
        U.S. 340.) can be found on many legal web sites by doing a
        Google search. Indeed, the broad availability of the text of
        [the U.S.] Supreme Court decisions is because they are not
        subject to copyright. The Feist decision reaffirmed the U.S.
        Copyright act of 1976 that ''there can be no copyright in
        facts''. The basis for the Feist decision can be found in the
        U.S. Constitution."

but I appreciate the P.P. folks point about explictly placing the data
in the public domain.

A place you can send your image data is to  
http://www.cellimagelibrary.org/


Best wishes, and may all your data be reused,


George



On 1/14/2012 2:47 PM, Michael Herron wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> PubSpectra needs Flash so it does not work on iPhone or iPad. Any plans to
> make it HTML5 compliant?
>
> On Saturday, January 14, 2012, Jason Swedlow<[hidden email]>  wrote:
>    
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> *****
>>
>> Hi-
>>
>> A few comments:
>>
>> George's PubSpectra resource is very nice.  The usage and contributions
>>      
> are
>    
>> exactly the kind of thing that can develop using open, shareable,
>> maintained resources.  I emphasise 'maintained' as anything like this must
>> be kept up-to-date for it to be at all useful.  George has done a great
>>      
> job
>    
>> with it.
>>
>> In OME, we provide many mechanism for storing data.  In fact, in our first
>> version of OME-XML, we imagined mechanisms for storing fluorescence
>> spectra.  As soon as we saw George's work, we were sooo happy that someone
>> else had taken this on, we presumed that a  URL linking to PubSpectra
>>      
> would
>    
>> provide the simplest, most flexible mechanism for storing spectral
>> information.  We haven't directly specified this, as we prefer to let
>>      
> users
>    
>> make these choices-- but we can.  In our current work, we are moving OMERO
>> to a stable platform in order to focus on delivering more functionality in
>> the clients (only if you really care,
>> http://trac.openmicroscopy.org.uk/ome/milestone/OMERO-Beta4.4).  Views of
>> PubSpectra data could certainly be implemented in the future.
>>
>> As always, comments, suggestions, and biting critiques are welcome at
>> http://www.openmicroscopy.org/community/
>>
>> And....hats off to Zeiss.  Very nice app!!!
>>
>> Cheers,
>>
>> Jason
>>
>>
>> On Sat, Jan 14, 2012 at 4:26 PM, George McNamara
>> <[hidden email]>wrote:
>>
>>      
>>> *****
>>> To join, leave or search the confocal microscopy listserv, go to:
>>> http://lists.umn.edu/cgi-bin/**wa?A0=confocalmicroscopy<
>>>        
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>
>    
>>> *****
>>>
>>> Hi Pete,
>>>
>>> I would match your $0.02 except that PubSpectra is open data access:
>>> freely available to you, Zeiss - it has been the source of the spectral
>>> Smart Setup in ZEN for years - and other vendors. Many vendors have
>>> contributed data, including LfieTech/Invitrogen/Molecular Probes, Chroma,
>>> Omega and Semrock, as have academics, including Roger Tsien/Robert
>>> Campbell, Jonathan Lindsey (see his photochemcad site). I have told many
>>> vendors about the data and encouraged them to include the data in their
>>> software. I congratulate Zeiss on their introduction of their iZeiss apps
>>> (I personally an not an i kind of guy).
>>>
>>> The PubSpectra data set can be downloaded in the ZIP file at the top of
>>> http://sylvester.org/shared-**resources/analytical-imaging/**
>>> links-forms-documentation/**pubspectra-data<
>>>        
> http://sylvester.org/shared-resources/analytical-imaging/links-forms-documentation/pubspectra-data
>    
>>      
>>> and the UA graphing site is http://www.spectra.arizona.**edu/<
>>>        
> http://www.spectra.arizona.edu/>- along with additional spectra that Urs
> Utzinger and Carl Boswell have
>    
>>> entered. Type in    2p   in the dye field for data at the UA site that is
>>> not currently in PubSpectra. Data from the UA site can even be
>>>        
> downloaded.
>    
>>> I'll go further an encourage OME, ImageJ / ImageJ2 / Fiji / MBF ImageJ,
>>> and other imaging developers, to make use of PubSpectra.
>>>
>>> Finally, I encourage everyone who has fluorescence and fluorescence
>>> related spectra (including, but limited to dyes, fluorescent proteins,
>>> filters, light sources), to send me data to add to PubSpectra -
>>>        
> preferably
>    
>>> in the same organization as is in the PubSpectra Excel 2007 (xlsx) file.
>>>
>>>
>>> George
>>>
>>>
>>> On 1/14/2012 7:18 AM, Peter Gabriel Pitrone wrote:
>>>
>>>        
>>>> *****
>>>> To join, leave or search the confocal microscopy listserv, go to:
>>>> http://lists.umn.edu/cgi-bin/**wa?A0=confocalmicroscopy<
>>>>          
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>
>    
>>>> *****
>>>>
>>>> I must say that I like the idea!
>>>>
>>>> However, I think that this would be better if Open Microscopy
>>>>          
> Environment
>    
>>>> would make a Smart Phone viewer so you wouldn't be limited by what
>>>> microscope system you acquired the data from to be able to see it.
>>>>
>>>> What I think is that the vendors really need to focus on right now is
>>>> compatibility, but I know that they think it is "Anathema".
>>>>
>>>> My $0.02 worth,
>>>>
>>>> Pete
>>>>
>>>> On Fri, January 13, 2012 4:26 pm, Johannes Amon wrote:
>>>> | *****
>>>> | To join, leave or search the confocal microscopy listserv, go to:
>>>> | http://lists.umn.edu/cgi-bin/**wa?A0=confocalmicroscopy<
>>>>          
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>
>    
>>>> | *****
>>>> |
>>>> | Dear Community,
>>>> |
>>>> | just to inform you, we at Carl Zeiss Microscopy just recently
>>>>          
> launched a
>    
>>>> | fluorescence microscopy app for your iPads, iPhones and iPod touch
>>>> | devices. I
>>>> | was already in contact with George McNamara as the app uses the
>>>> pubspectra
>>>> | database, similar to our ZEN Smart Setup, and he suggested to post it
>>>> here
>>>> | so
>>>> | that you are able to have a test-drive and discuss what you like or
>>>>          
> what
>    
>>>> | you
>>>> | might not like. We are completely open for ideas, so hit the inbox
>>>> micro-
>>>> | [hidden email], hit me, and of course also feel free to discuss the app
>>>> | here.
>>>> |
>>>> | http://www.zeiss.com/micro-**apps<http://www.zeiss.com/micro-apps>
>>>> |
>>>> | The website should give you a good impression about what the app is
>>>>          
> able
>    
>>>> | to
>>>> | do. We are really curious to learn how it will be received by the
>>>> | scientific
>>>> | community so I'll try to check back regularly and see what you think.
>>>> |
>>>> | Have a nice weekend!
>>>> |
>>>> | Carl Zeiss MicroImaging GmbH
>>>> | Business Unit BioSciences
>>>> | Imaging Software Munich
>>>> |
>>>> | Dr. Johannes Amon
>>>> | [hidden email]
>>>> |
>>>>
>>>>
>>>>
>>>>
>>>>          
>>>
>>> --
>>>
>>>
>>> George McNamara, PhD
>>> Analytical Imaging Core Facility
>>> University of Miami
>>>
>>>        
>>
>>
>> --
>> **************************
>> Wellcome Trust Centre for Gene Regulation&  Expression
>> College of Life Sciences
>> MSI/WTB/JBC Complex
>> University of Dundee
>> Dow Street
>> Dundee  DD1 5EH
>> United Kingdom
>>
>> phone [phone]
>> Intl phone:  [phone]
>> FAX   [phone]
>> email: [hidden email]
>>
>> Lab Page: http://www.lifesci.dundee.ac.uk/gre/staff/jason-swedlow
>> Open Microscopy Environment: http://openmicroscopy.org
>> **************************
>>
>>      
>    

--


George McNamara, PhD
Analytical Imaging Core Facility
University of Miami

[Johannes Amon]

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

Dear Peter,

right from the beginning we designed our iOS app so that every microscopist independently
of the system in his lab is able to use our spectra viewer and can configure all the filters and
presets tailored to his very own experimental setup. while Light Lab includes some ZEISS-
specific presets (and might include some more in future updates) this is completely for
convenience and as a service to users of our systems.

we encourage every microscopist to use Light Lab with his own system settings no matter
from which vendor your system or filters are. and if I might add, I really fought hard for the
free configuration options ^^

in 2012 we have some interesting new projects centered around George's database, so give
us a little time here. and please don't be afraid that we'd try to 'own' pubspectra: our main
interest lies in establishing a standard database source and format for the whole scientific
community together with you. we deeply respect the work George has put into pubspectra
and we value the 'open source' spirit behind it. a well-maintained standardized database
with an open file format (xml, anybody?) and an easy-to-use open source windows GUI  
makes our work easier, it makes your work easier, and we don't care too much if it also
makes the work of our competitors' easier.

stay with us, and have a nice evening!

[Adrian Smith-6]

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

On 14/01/2012, at 9:01 PM, Johannes Amon wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> of course I can't tell you any specifics but at the moment we are evaluating a native port to
> android ICS 4.0. at the end it always comes down to budget so it would help immensely if
> you'd order some confocals right now ^^
>
> just joking, gonna keep you posted on this project

I would love to find a decent resolution calculator that can be used on a smartphone/tablet (iOS preferably for me :)

Add in various options for different digitisation approaches (PMT, cameras) with Nyquist shortcuts and it would be real winner…

Regards,

Adrian Smith
Centenary Institute, Sydney, Australia

[Peter Gabriel Pitrone]

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

Dear Johannes,

I misunderstood the whole concept of the app. I thought it would only work
with acquired data, if it is a stand alone spectral viewer than that
really is a great idea. Don't forget the light sources!!

I also wish you a great weekend and week ahead,

Pete

On Sun, January 15, 2012 2:00 am, Johannes Amon wrote:
| *****
| To join, leave or search the confocal microscopy listserv, go to:
| http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
| *****
|
| Dear Peter,
|
| right from the beginning we designed our iOS app so that every
| microscopist independently
| of the system in his lab is able to use our spectra viewer and can
| configure all the filters and
| presets tailored to his very own experimental setup. while Light Lab
| includes some ZEISS-
| specific presets (and might include some more in future updates) this is
| completely for
| convenience and as a service to users of our systems.
|
| we encourage every microscopist to use Light Lab with his own system
| settings no matter
| from which vendor your system or filters are. and if I might add, I really
| fought hard for the
| free configuration options ^^
|
| in 2012 we have some interesting new projects centered around George's
| database, so give
| us a little time here. and please don't be afraid that we'd try to 'own'
| pubspectra: our main
| interest lies in establishing a standard database source and format for
| the whole scientific
| community together with you. we deeply respect the work George has put
| into pubspectra
| and we value the 'open source' spirit behind it. a well-maintained
| standardized database
| with an open file format (xml, anybody?) and an easy-to-use open source
| windows GUI
| makes our work easier, it makes your work easier, and we don't care too
| much if it also
| makes the work of our competitors' easier.
|
| stay with us, and have a nice evening!
|


--
Peter Gabriel Pitrone - TechRMS
Microscopy/Imaging Specialist
Prof. Dr. Pavel Tomancak group
Max Planck Institute for
Molecular Biology and Genetics
Pfotenhauerstr. 108
01307 Dresden

"If a straight line fit is required, obtain only two data points." - Anon.

[John Oreopoulos]

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

Adrian, there is a fairly good iPhone application that does some of the things you mentioned. It's called ResCalc.

John Oreopoulos
Research Assistant
Spectral Applied Research
Richmond Hill, Ontario
Canada
www.spectral.ca

On 2012-01-15, at 1:03 AM, Adrian Smith <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> On 14/01/2012, at 9:01 PM, Johannes Amon wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> *****
>>
>> of course I can't tell you any specifics but at the moment we are evaluating a native port to
>> android ICS 4.0. at the end it always comes down to budget so it would help immensely if
>> you'd order some confocals right now ^^
>>
>> just joking, gonna keep you posted on this project
>
>
> I would love to find a decent resolution calculator that can be used on a smartphone/tablet (iOS preferably for me :)
>
> Add in various options for different digitisation approaches (PMT, cameras) with Nyquist shortcuts and it would be real winner…
>
> Regards,
>
> Adrian Smith
> Centenary Institute, Sydney, Australia

[Tim Feinstein-2]

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

Hi John,

ResCalc is a nice app, but it seems to calculate res and nyquist for widefield microscopy only.  Am I wrong about that?  As it is I use the Nyquist calculator on the SVI site (no commercial interest) but I would love to have something off-line.  

Cheers,


TIm Feinstein

Sent from my iPad

On Jan 15, 2012, at 10:40 AM, John Oreopoulos <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Adrian, there is a fairly good iPhone application that does some of the things you mentioned. It's called ResCalc.
>
> John Oreopoulos
> Research Assistant
> Spectral Applied Research
> Richmond Hill, Ontario
> Canada
> www.spectral.ca
>
> On 2012-01-15, at 1:03 AM, Adrian Smith <[hidden email]> wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> *****
>>
>> On 14/01/2012, at 9:01 PM, Johannes Amon wrote:
>>
>>> *****
>>> To join, leave or search the confocal microscopy listserv, go to:
>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>>> *****
>>>
>>> of course I can't tell you any specifics but at the moment we are evaluating a native port to
>>> android ICS 4.0. at the end it always comes down to budget so it would help immensely if
>>> you'd order some confocals right now ^^
>>>
>>> just joking, gonna keep you posted on this project
>>
>>
>> I would love to find a decent resolution calculator that can be used on a smartphone/tablet (iOS preferably for me :)
>>
>> Add in various options for different digitisation approaches (PMT, cameras) with Nyquist shortcuts and it would be real winner…
>>
>> Regards,
>>
>> Adrian Smith
>> Centenary Institute, Sydney, Australia

[Guy Cox-2]

There isn't any difference between widefield and confocal resolution in any normal fluorescence mode.   Do you really need an app to work out 0.61 lambda/NA?  And then to divide by 2.3 to get Nyquist?  If you are in multiphoton it's a little more complicated since root 2 (1.414) comes in, but you can just use the formula 0.43 lambda / NA.  

                                        Guy

Optical Imaging Techniques in Cell Biology
by Guy Cox    CRC Press / Taylor & Francis
     http://www.guycox.com/optical.htm
______________________________________________
Guy Cox, MA, DPhil(Oxon), Honorary Associate,
Australian Centre for Microscopy & Microanalysis,
Madsen Building F09, University of Sydney, NSW 2006

Phone [phone]     Fax [phone]
             Mobile [phone]
______________________________________________
      http://www.guycox.net
 

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Tim Feinstein
Sent: Monday, 16 January 2012 4:54 AM
To: [hidden email]
Subject: Re: Light Lab by Carl Zeiss Microscopy for iOS devices

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

Hi John,

ResCalc is a nice app, but it seems to calculate res and nyquist for widefield microscopy only.  Am I wrong about that?  As it is I use the Nyquist calculator on the SVI site (no commercial interest) but I would love to have something off-line.  

Cheers,


TIm Feinstein

Sent from my iPad

On Jan 15, 2012, at 10:40 AM, John Oreopoulos <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Adrian, there is a fairly good iPhone application that does some of the things you mentioned. It's called ResCalc.
>
> John Oreopoulos
> Research Assistant
> Spectral Applied Research
> Richmond Hill, Ontario
> Canada
> www.spectral.ca
>
> On 2012-01-15, at 1:03 AM, Adrian Smith <[hidden email]> wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> *****
>>
>> On 14/01/2012, at 9:01 PM, Johannes Amon wrote:
>>
>>> *****
>>> To join, leave or search the confocal microscopy listserv, go to:
>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>>> *****
>>>
>>> of course I can't tell you any specifics but at the moment we are evaluating a native port to
>>> android ICS 4.0. at the end it always comes down to budget so it would help immensely if
>>> you'd order some confocals right now ^^
>>>
>>> just joking, gonna keep you posted on this project
>>
>>
>> I would love to find a decent resolution calculator that can be used on a smartphone/tablet (iOS preferably for me :)
>>
>> Add in various options for different digitisation approaches (PMT, cameras) with Nyquist shortcuts and it would be real winner…
>>
>> Regards,
>>
>> Adrian Smith
>> Centenary Institute, Sydney, Australia

[John Oreopoulos]

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

Tim, the ResCalc app assumes a Nyquist sampling rate of 2.3x.

As for whether or not one should choose their image pixel size using this sampling factor of 2.3 or something else for confocal or widefield, I would refer the interested reader to the epic discussion on this topic back from 2007 (so as not to have it repeated again!):

http://lists.umn.edu/cgi-bin/wa?A2=ind0701&L=CONFOCALMICROSCOPY&D=0&P=15141

John Oreopoulos


On 2012-01-15, at 8:08 PM, Guy Cox wrote:

> There isn't any difference between widefield and confocal resolution in any normal fluorescence mode.   Do you really need an app to work out 0.61 lambda/NA?  And then to divide by 2.3 to get Nyquist?  If you are in multiphoton it's a little more complicated since root 2 (1.414) comes in, but you can just use the formula 0.43 lambda / NA.  
>
> Guy
>
> Optical Imaging Techniques in Cell Biology
> by Guy Cox    CRC Press / Taylor & Francis
>     http://www.guycox.com/optical.htm
> ______________________________________________
> Guy Cox, MA, DPhil(Oxon), Honorary Associate,
> Australian Centre for Microscopy & Microanalysis,
> Madsen Building F09, University of Sydney, NSW 2006
>
> Phone [phone]     Fax [phone]
>             Mobile [phone]
> ______________________________________________
>      http://www.guycox.net
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Tim Feinstein
> Sent: Monday, 16 January 2012 4:54 AM
> To: [hidden email]
> Subject: Re: Light Lab by Carl Zeiss Microscopy for iOS devices
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi John,
>
> ResCalc is a nice app, but it seems to calculate res and nyquist for widefield microscopy only.  Am I wrong about that?  As it is I use the Nyquist calculator on the SVI site (no commercial interest) but I would love to have something off-line.  
>
> Cheers,
>
>
> TIm Feinstein
>
> Sent from my iPad
>
> On Jan 15, 2012, at 10:40 AM, John Oreopoulos <[hidden email]> wrote:
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> *****
>>
>> Adrian, there is a fairly good iPhone application that does some of the things you mentioned. It's called ResCalc.
>>
>> John Oreopoulos
>> Research Assistant
>> Spectral Applied Research
>> Richmond Hill, Ontario
>> Canada
>> www.spectral.ca
>>
>> On 2012-01-15, at 1:03 AM, Adrian Smith <[hidden email]> wrote:
>>
>>> *****
>>> To join, leave or search the confocal microscopy listserv, go to:
>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>>> *****
>>>
>>> On 14/01/2012, at 9:01 PM, Johannes Amon wrote:
>>>
>>>> *****
>>>> To join, leave or search the confocal microscopy listserv, go to:
>>>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>>>> *****
>>>>
>>>> of course I can't tell you any specifics but at the moment we are evaluating a native port to
>>>> android ICS 4.0. at the end it always comes down to budget so it would help immensely if
>>>> you'd order some confocals right now ^^
>>>>
>>>> just joking, gonna keep you posted on this project
>>>
>>>
>>> I would love to find a decent resolution calculator that can be used on a smartphone/tablet (iOS preferably for me :)
>>>
>>> Add in various options for different digitisation approaches (PMT, cameras) with Nyquist shortcuts and it would be real winner…
>>>
>>> Regards,
>>>
>>> Adrian Smith
>>> Centenary Institute, Sydney, Australia

[Steffen Dietzel]

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

Well, for my part I wouldn't mind an (Android) app for

- z-resolution, prefereably one that includes 2- and 3-photon excitation
and

- resolution and brightness at various depths under refraction index
mismatch conditions (e.g. sample embedded in glycerol instead of
immersion oil or underneath a coverslip with a dipping objective).

Life isn't always as simple as 0.61 lambda/NA.


Even better though than a bunch of apps for various systems would a
calculator running in a web browser based on common standards so that it
would be accessible on every system.


Steffen


On 16.01.2012 02:08, Guy Cox wrote:

> There isn't any difference between widefield and confocal resolution in any normal fluorescence mode.   Do you really need an app to work out 0.61 lambda/NA?  And then to divide by 2.3 to get Nyquist?  If you are in multiphoton it's a little more complicated since root 2 (1.414) comes in, but you can just use the formula 0.43 lambda / NA.
>
> Guy
>
> Optical Imaging Techniques in Cell Biology
> by Guy Cox    CRC Press / Taylor&  Francis
>       http://www.guycox.com/optical.htm
> ______________________________________________
> Guy Cox, MA, DPhil(Oxon), Honorary Associate,
> Australian Centre for Microscopy&  Microanalysis,
> Madsen Building F09, University of Sydney, NSW 2006
>
> Phone [phone]     Fax [phone]
>               Mobile [phone]
> ______________________________________________
>        http://www.guycox.net
>

--
------------------------------------------------------------
Steffen Dietzel, PD Dr. rer. nat
Ludwig-Maximilians-Universität München
Walter-Brendel-Zentrum für experimentelle Medizin (WBex)
Head of light microscopy

Mail room:
Marchioninistr. 15, D-81377 München

Building location:
Marchioninistr. 27,  München-Großhadern