Re: CONFOCALMICROSCOPY Digest - 17 Nov 2011 to 18 Nov 2011 (#2011-88)

[Emma King-2]

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Hi All,

Thanks for all your messages. Louis described much better than I did what we plan to do "In fact you want to add multiple Z-series together in order to form one huge series"!

 We have Volocity (and obviously imageJ) to visualise 3D data and I believe we can add z-series together, on top of each other. My worry is we will have issues aligning structures in one z-stack, from one tissue section, with the same structures in the next z-stack/tissue section.

I'll give it a go using the suggestions made and come back to you if I get stuck!

Thanks again,
Em

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of CONFOCALMICROSCOPY automatic digest system
Sent: 19 November 2011 06:05
To: [hidden email]
Subject: CONFOCALMICROSCOPY Digest - 17 Nov 2011 to 18 Nov 2011 (#2011-88)

There are 12 messages totalling 698 lines in this issue.

Topics of the day:

  1. 3D reconstruction of multiple, fluorescently labelled, sections (3)
  2. RE 3D reconstruction of multiple, fluorescently labelled, sections (3)
  3. Olympus Corp in financial trouble? (2)
  4. (lots) more on Olympus
  5. Cell viability assay
  6. Fast two-photon imaging: Constant fraction discriminator and variable
     delay for Laser pulse-synch
  7. Olympus Corp in financial trouble? We certainly hope not!

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

Date:    Fri, 18 Nov 2011 08:39:57 -0600
From:    Emma King <[hidden email]>
Subject: 3D reconstruction of multiple, fluorescently labelled, sections

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We would like to take serial sections (20 microns thick) of rat spinal=20=

cord (up to 1cm long), label them with a bright and specific fluorescent=20=

label, acquire images (we can use either a widefield or confocal=20
microscope) and then reconstruct the data in to one, 3D structure.=20

We have the sectioning, staining and acquisition parameters/options=20
under control, but don't have any software capable of reconstructing=20
the resultant images. Does anyone have any suggestions as to what=20
software to use and where to get it from?=20

Any help much appreciated.=20

Cheers,=20
Emma=20

Advanced Microscopy Unit=20
School of Biomedical Sciences=20
Univeristy of Nottingham

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

Date:    Fri, 18 Nov 2011 09:51:43 -0500
From:    [hidden email]
Subject: RE 3D reconstruction of multiple, fluorescently labelled, sections

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Hi Emma,

In fact you want to add mutltiple Z-series together in order to form one=20
huge serie.  First, you will need a good computer and 2nd, I have done it=20
using Huygens software (SVI).=20
Also, I am pretty sure that there is a plugin In" Image J" that can do=20
that.  Do not forget to do that with a good computer!!!!

Best regards,

Louis

Louis Villeneuve
Associ=E9 de recherche - Microscopie confocale
Institut de Cardiologie de Montreal- Centre de recherche
5000 est B=E9langer
Montreal (Qc), Canada
H1T 3C8

514-376-3330 ext 3511=20
514-376-1355 (fax)



Emma King <[hidden email]>@LISTS.UMN.EDU=20
Envoy=E9 par : Confocal Microscopy List <[hidden email]>
2011-11-18 09:39
Veuillez r=E9pondre =E0
Confocal Microscopy List <[hidden email]>


A
[hidden email]
cc

Objet
3D reconstruction of multiple, fluorescently labelled, sections








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We would like to take serial sections (20 microns thick) of rat spinal=20
cord (up to 1cm long), label them with a bright and specific fluorescent=20
label, acquire images (we can use either a widefield or confocal=20
microscope) and then reconstruct the data in to one, 3D structure.=20

We have the sectioning, staining and acquisition parameters/options=20
under control, but don't have any software capable of reconstructing=20
the resultant images. Does anyone have any suggestions as to what=20
software to use and where to get it from?=20

Any help much appreciated.=20

Cheers,=20
Emma=20

Advanced Microscopy Unit=20
School of Biomedical Sciences=20
Univeristy of Nottingham

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

Date:    Fri, 18 Nov 2011 09:56:23 -0500
From:    Louis Kerr <[hidden email]>
Subject: Re: 3D reconstruction of multiple, fluorescently labelled, sections

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Hi Emma,

Have you seen the work from Stephen Smith's Lab at Stanford with array tomography? This is a link to a Cold Spring Harbor Protocol.

http :// cshprotocols . cshlp .org/content/2010/11/ pdb .top89.full

Good luck,
Louie

----- Original Message -----
From: "Emma King" < emma .[hidden email]>
To: CONFOCALMICROSCOPY @LISTS. UMN . EDU
Sent: Friday, November 18, 2011 9:39:57 AM
Subject: 3D reconstruction of multiple, fluorescently labelled , sections

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We would like to take serial sections (20 microns thick) of rat spinal
cord (up to 1cm long), label them with a bright and specific fluorescent
label, acquire images (we can use either a widefield or confocal
microscope) and then reconstruct the data in to one, 3D structure.

We have the sectioning, staining and acquisition parameters/options
under control, but don't have any software capable of reconstructing
the resultant images. Does anyone have any suggestions as to what
software to use and where to get it from?

Any help much appreciated.

Cheers,
Emma

Advanced Microscopy Unit
School of Biomedical Sciences
Univeristy of Nottingham


--



Louis Kerr
lkerr @ mbl . edu

Research and Education Support Coordinator
Marine Biological Laboratory
7 MBL Street
Woods Hole, MA 02543
508-289-7273
508-540-6902 (FAX)
508-292-0289 (Cell phone)

VISIT OUR WEB SITES:
www . mbl . edu
www .courses. mbl . edu

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

Date:    Fri, 18 Nov 2011 16:51:30 +0100
From:    Tineke Vendrig <[hidden email]>
Subject: Re: 3D reconstruction of multiple, fluorescently labelled, sections

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We use the Andor software for our 3D movies, works nice and good!

Tineke Vendrig

--
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technical engineer optical microscopy
Delft University of Technology
Bionano Science
Kavli Institute of Nanoscience
Lorentzweg 1
2628LJ Delft
room F185
Tel: [phone]
Fax:[phone]
email: [hidden email]
mobile phone: [phone]


2011/11/18 Emma King <[hidden email]>

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> We would like to take serial sections (20 microns thick) of rat spinal
> cord (up to 1cm long), label them with a bright and specific fluorescent
> label, acquire images (we can use either a widefield or confocal
> microscope) and then reconstruct the data in to one, 3D structure.
>
> We have the sectioning, staining and acquisition parameters/options
> under control, but don't have any software capable of reconstructing
> the resultant images. Does anyone have any suggestions as to what
> software to use and where to get it from?
>
> Any help much appreciated.
>
> Cheers,
> Emma
>
> Advanced Microscopy Unit
> School of Biomedical Sciences
> Univeristy of Nottingham
>

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

Date:    Fri, 18 Nov 2011 12:28:12 -0500
From:    "Cammer, Michael" <[hidden email]>
Subject: Olympus Corp in financial trouble?

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"Japanese officials say that at least $4.9 billion is unaccounted for in a =
financial scandal at Olympus<http://topics.nytimes.com/top/news/business/co=
mpanies/olympus_corporation/index.html?inline=3Dnyt-org> and are investigat=
ing whether much of that money went to companies with links to organized cr=
ime."
http://www.nytimes.com/2011/11/18/business/global/japanese-police-investiga=
te-olympus.html?_r=3D1&scp=3D3&sq=3Dolympus&st=3Dcse


________________________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: [phone]  Cell: [phone]

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

Date:    Fri, 18 Nov 2011 12:18:55 -0600
From:    Johannes Schindelin <[hidden email]>
Subject: Re: RE 3D reconstruction of multiple, fluorescently labelled, sections

  This message is in MIME format.  The first part should be readable text,
  while the remaining parts are likely unreadable without MIME-aware tools.

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Content-transfer-encoding: 8BIT

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On Fri, 18 Nov 2011, [hidden email] wrote:

> Emma King <[hidden email]>@LISTS.UMN.EDU
> Envoyé par : Confocal Microscopy List <[hidden email]>
> 2011-11-18 09:39
>
> > We would like to take serial sections (20 microns thick) of rat spinal
> > cord (up to 1cm long), label them with a bright and specific
> > fluorescent label, acquire images (we can use either a widefield or
> > confocal microscope) and then reconstruct the data in to one, 3D
> > structure.
>
> > We have the sectioning, staining and acquisition parameters/options
> > under control, but don't have any software capable of reconstructing
> > the resultant images. Does anyone have any suggestions as to what
> > software to use and where to get it from?
>
> In fact you want to add mutltiple Z-series together in order to form one
> huge serie.  First, you will need a good computer and 2nd, I have done
> it using Huygens software (SVI).
>
> Also, I am pretty sure that there is a plugin In" Image J" that can do
> that.  Do not forget to do that with a good computer!!!!

If all you want to do is a volume rendering, there are indeed 2 ImageJ
plugins to do the job: Volume Viewer (non-accelerated) and 3D Viewer (this
one uses your graphics adapter's accelerated 3D rendering).

However, if you need to have surface models, you might want to look into
the TrakEM2 plugin. It is very powerful, therefore it takes some training
before one can exploit its capabilities in full.

If you do not want to bother to find all the bits and pieces required for
these plugins to run, please feel free to download Fiji (http://fiji.sc/)
which bundles ImageJ with a lot of plugins (including the 3 mentioned
above).

Ciao,
Johannes

--Boundary_(ID_BmV8ySyi3ZWYFpVvpZWp+A)--

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

Date:    Fri, 18 Nov 2011 11:02:21 -0800
From:    "Armstrong, Brian" <[hidden email]>
Subject: Re: RE 3D reconstruction of multiple, fluorescently labelled, sections

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You could try Reconstruct from NIH Human Brain project =
(http://synapses.clm.utexas.edu/tools/reconstruct/reconstruct.stm ).

In my opinion, Amira, Imaris, and Volocity, are probably best at 3D =
visualization tools.=20

Cheers,

Brian D Armstrong PhD
Assistant Research Professor
Light Microscopy Core=20
Beckman Research Institute
City of Hope
Dept of Neuroscience
1450 E Duarte Rd
Duarte, CA 91010
626-256-4673 x62872

http://www.cityofhope.org/research/support/Light-Microscopy-Digital-Imaging=
/Pages/default.aspx


-----Original Message-----
=46rom: Confocal Microscopy List [mailto:[hidden email]] =
=
On Behalf Of Johannes Schindelin
Sent: Friday, November 18, 2011 10:19 AM
To: [hidden email]
Subject: Re: RE 3D reconstruction of multiple, fluorescently labelled, =
sections

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On Fri, 18 Nov 2011, [hidden email] wrote:

> Emma King <[hidden email]>@LISTS.UMN.EDU=20
> Envoy=E9 par : Confocal Microscopy List <[hidden email]>
> 2011-11-18 09:39
>
> > We would like to take serial sections (20 microns thick) of rat spinal
> > cord (up to 1cm long), label them with a bright and specific
> > fluorescent label, acquire images (we can use either a widefield or
> > confocal microscope) and then reconstruct the data in to one, 3D
> > structure.=20
>=20
> > We have the sectioning, staining and acquisition parameters/options
> > under control, but don't have any software capable of reconstructing
> > the resultant images. Does anyone have any suggestions as to what
> > software to use and where to get it from=3F=20
>=20
> In fact you want to add mutltiple Z-series together in order to form one
> huge serie.  First, you will need a good computer and 2nd, I have done
> it using Huygens software (SVI).=20
>
> Also, I am pretty sure that there is a plugin In" Image J" that can do=20
> that.  Do not forget to do that with a good computer!!!!

If all you want to do is a volume rendering, there are indeed 2 ImageJ
plugins to do the job: Volume Viewer (non-accelerated) and 3D Viewer (this
one uses your graphics adapter's accelerated 3D rendering).

However, if you need to have surface models, you might want to look into
the TrakEM2 plugin. It is very powerful, therefore it takes some training
before one can exploit its capabilities in full.

If you do not want to bother to find all the bits and pieces required for
these plugins to run, please feel free to download Fiji (http://fiji.sc/)
which bundles ImageJ with a lot of plugins (including the 3 mentioned
above).

Ciao,
Johannes


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

Date:    Fri, 18 Nov 2011 13:24:11 -0600
From:    Martin Wessendorf <[hidden email]>
Subject: Re: Olympus Corp in financial trouble?

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Michael et al--

On 11/18/2011 11:28 AM, Cammer, Michael wrote:

> "Japanese officials say that at least $4.9 billion is unaccounted for in a financial scandal at Olympus<http://topics.nytimes.com/top/news/business/companies/olympus_corporation/index.html?inline=nyt-org>  and are investigating whether much of that money went to companies with links to organized crime."
> http://www.nytimes.com/2011/11/18/business/global/japanese-police-investigate-olympus.html?_r=1&scp=3&sq=olympus&st=cse

I've seen these reports, too, over the past few weeks.  However,
although it seems quite likely that their stockholders will be unhappy
with them, it's unclear (to me, at least!) that the company is in
financial trouble yet.

Disclaimer: I'm definitely not a certified financial advisor!

Martin Wessendorf
--
Martin Wessendorf, Ph.D.                   office: [phone]
Assoc Prof, Dept Neuroscience                 lab: [phone]
University of Minnesota             Preferred FAX: [phone]
6-145 Jackson Hall, 321 Church St. SE    Dept Fax: [phone]
Minneapolis, MN  55455                    e-mail: [hidden email]

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

Date:    Fri, 18 Nov 2011 15:26:43 -0600
From:    Martin Wessendorf <[hidden email]>
Subject: (lots) more on Olympus

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For anyone who's interested:

http://newsfeedresearcher.com/data/articles_b47/olympus-woodford-company.html

Martin
--
Martin Wessendorf, Ph.D.                   office: [phone]
Assoc Prof, Dept Neuroscience                 lab: [phone]
University of Minnesota             Preferred FAX: [phone]
6-145 Jackson Hall, 321 Church St. SE    Dept Fax: [phone]
Minneapolis, MN  55455                    e-mail: [hidden email]

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

Date:    Fri, 18 Nov 2011 14:34:04 -0800
From:    Iain Johnson <[hidden email]>
Subject: Re: Cell viability assay

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Calcein AM  (intracellular esterase substrate).  Incubate cells for 10
minutes in 1 microM calcein AM in serum-free medium at 37C.  Wash off
staining medium and replace with complete culture medium.  Image in
FITC/GFP channel.

You can also add a second dimension to the assay (at the expense of giving
up more spectral real estate).

SYTOX Orange (Molecular Probes; membrane permeability probe).  Add to
complete culture medium at 5 microM.  Do not wash.  Image in TRITC/Cy3
channel.

Iain

Iain Johnson Consulting
Eugene, OR
[phone]

On Thu, Nov 17, 2011 at 7:23 AM, B. Prabhakar Pandian <[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>
> *****
>
> Hello,
>             I am emailing to see if anybody has a suggestion for a cell
> viability/toxicity assay that works similar to LDH/Caspase but relies on
> internal enzymes rather than in the supernatant.  In addition, it should be
> compatible with fluorescence microscope.
>
> Thanks,
>
> -Prabhakar
>

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

Date:    Fri, 18 Nov 2011 19:50:53 -0500
From:    Christian Wilms <[hidden email]>
Subject: Re: Fast two-photon imaging: Constant fraction discriminator and variable delay for Laser pulse-synch

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Regarding the delay: if you do not need it to flexible in timing,
simply getting a coaxial cable of the correct length (20 cm
corresponds roughly to 1 ns) is one option. A bit more flexible and
still affordable are variable delay lines such as the Ortec 425 <http://www.ortec-online.com/download/425A.pdf

Best, Christian

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

Date:    Fri, 18 Nov 2011 23:08:24 -0500
From:    "Alison J. North" <[hidden email]>
Subject: Re: Olympus Corp in financial trouble? We certainly hope not!

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Hey Michael,

There is no question that Olympus has been going through hell this year - s=
tarting with the tsunami, and who could have guessed that things could have=
 got even worse because of a few crooks (worst case) or idiots (best case) =
at the top....   Given that we own several high-end Olympus microscopes, we=
 obviously have a vested interest in the company staying afloat and are und=
erstandably all concerned.  More than that though, I have worked with the s=
ame Olympus team for over 11 years now and they have not only proved to be =
great colleagues but also good friends - we have caught wild mice on our ha=
nds and knees in my lab together, I have played despicable April Fool's jok=
es on them (well truthfully, only once - they have refused to visit my lab =
on April 1st ever since), and they have proved themselves such wizards at s=
olving the most mysterious and intractable microscope problems that we nick=
named the two local guys Dumbledore and Gandalf.  At this point I think any=
 discussion of what will happen is just pointless speculation, and one whic=
h they cannot possibly enter into, so the best we can do is to trust this w=
ill all blow over eventually and offer the microscope guys our support, say=
ing: we're rooting for you, and here's to 2012 being a far better year for =
you than 2011!

Best,
Alison
P.S.  Sorry if I'm gushing to the confocal listserver - blame the glass of =
wine in my hand and the fact that I just came back from the movies :-).=20

  =20
________________________________________
From: Confocal Microscopy List [[hidden email]] On Behalf=
 Of Cammer, Michael [[hidden email]]
Sent: Friday, November 18, 2011 12:28 PM
To: [hidden email]
Subject: Olympus Corp in financial trouble?

*****
To join, leave or search the confocal microscopy listserv, go to:
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"Japanese officials say that at least $4.9 billion is unaccounted for in a =
financial scandal at Olympus<http://topics.nytimes.com/top/news/business/co=
mpanies/olympus_corporation/index.html?inline=3Dnyt-org> and are investigat=
ing whether much of that money went to companies with links to organized cr=
ime."
http://www.nytimes.com/2011/11/18/business/global/japanese-police-investiga=
te-olympus.html?_r=3D1&scp=3D3&sq=3Dolympus&st=3Dcse


________________________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: [phone]  Cell: [phone]

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End of CONFOCALMICROSCOPY Digest - 17 Nov 2011 to 18 Nov 2011 (#2011-88)
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Hi Emma,

You are correct, histological sections can be a problem because as sections deform, alignment often requires transformation/rotation as well as translation.  This recent paper in Traffic describes a new ImageJ tool that could provide what you need:

http://onlinelibrary.wiley.com/doi/10.1111/j.1600-0854.2011.01309.x/abstract

After alignment is resolved I agree that ImageJ/Fiji can handle 3d data presentation with little problem.  

All the best,


Tim Feinstein

Sent from my iPad

On Nov 21, 2011, at 4:18 AM, Emma King <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi All,
>
> Thanks for all your messages. Louis described much better than I did what we plan to do "In fact you want to add multiple Z-series together in order to form one huge series"!
>
> We have Volocity (and obviously imageJ) to visualise 3D data and I believe we can add z-series together, on top of each other. My worry is we will have issues aligning structures in one z-stack, from one tissue section, with the same structures in the next z-stack/tissue section.
>
> I'll give it a go using the suggestions made and come back to you if I get stuck!
>
> Thanks again,
> Em
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of CONFOCALMICROSCOPY automatic digest system
> Sent: 19 November 2011 06:05
> To: [hidden email]
> Subject: CONFOCALMICROSCOPY Digest - 17 Nov 2011 to 18 Nov 2011 (#2011-88)
>
> There are 12 messages totalling 698 lines in this issue.
>
> Topics of the day:
>
>  1. 3D reconstruction of multiple, fluorescently labelled, sections (3)
>  2. RE 3D reconstruction of multiple, fluorescently labelled, sections (3)
>  3. Olympus Corp in financial trouble? (2)
>  4. (lots) more on Olympus
>  5. Cell viability assay
>  6. Fast two-photon imaging: Constant fraction discriminator and variable
>     delay for Laser pulse-synch
>  7. Olympus Corp in financial trouble? We certainly hope not!
>
> ----------------------------------------------------------------------
>
> Date:    Fri, 18 Nov 2011 08:39:57 -0600
> From:    Emma King <[hidden email]>
> Subject: 3D reconstruction of multiple, fluorescently labelled, sections
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=3Dconfocalmicroscopy
> *****
>
> We would like to take serial sections (20 microns thick) of rat spinal=20=
>
> cord (up to 1cm long), label them with a bright and specific fluorescent=20=
>
> label, acquire images (we can use either a widefield or confocal=20
> microscope) and then reconstruct the data in to one, 3D structure.=20
>
> We have the sectioning, staining and acquisition parameters/options=20
> under control, but don't have any software capable of reconstructing=20
> the resultant images. Does anyone have any suggestions as to what=20
> software to use and where to get it from?=20
>
> Any help much appreciated.=20
>
> Cheers,=20
> Emma=20
>
> Advanced Microscopy Unit=20
> School of Biomedical Sciences=20
> Univeristy of Nottingham
>
> ------------------------------
>
> Date:    Fri, 18 Nov 2011 09:51:43 -0500
> From:    [hidden email]
> Subject: RE 3D reconstruction of multiple, fluorescently labelled, sections
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=3Dconfocalmicroscopy
> *****
>
> Hi Emma,
>
> In fact you want to add mutltiple Z-series together in order to form one=20
> huge serie.  First, you will need a good computer and 2nd, I have done it=20
> using Huygens software (SVI).=20
> Also, I am pretty sure that there is a plugin In" Image J" that can do=20
> that.  Do not forget to do that with a good computer!!!!
>
> Best regards,
>
> Louis
>
> Louis Villeneuve
> Associ=E9 de recherche - Microscopie confocale
> Institut de Cardiologie de Montreal- Centre de recherche
> 5000 est B=E9langer
> Montreal (Qc), Canada
> H1T 3C8
>
> 514-376-3330 ext 3511=20
> 514-376-1355 (fax)
>
>
>
> Emma King <[hidden email]>@LISTS.UMN.EDU=20
> Envoy=E9 par : Confocal Microscopy List <[hidden email]>
> 2011-11-18 09:39
> Veuillez r=E9pondre =E0
> Confocal Microscopy List <[hidden email]>
>
>
> A
> [hidden email]
> cc
>
> Objet
> 3D reconstruction of multiple, fluorescently labelled, sections
>
>
>
>
>
>
>
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=3Dconfocalmicroscopy
> *****
>
> We would like to take serial sections (20 microns thick) of rat spinal=20
> cord (up to 1cm long), label them with a bright and specific fluorescent=20
> label, acquire images (we can use either a widefield or confocal=20
> microscope) and then reconstruct the data in to one, 3D structure.=20
>
> We have the sectioning, staining and acquisition parameters/options=20
> under control, but don't have any software capable of reconstructing=20
> the resultant images. Does anyone have any suggestions as to what=20
> software to use and where to get it from?=20
>
> Any help much appreciated.=20
>
> Cheers,=20
> Emma=20
>
> Advanced Microscopy Unit=20
> School of Biomedical Sciences=20
> Univeristy of Nottingham
>
> ------------------------------
>
> Date:    Fri, 18 Nov 2011 09:56:23 -0500
> From:    Louis Kerr <[hidden email]>
> Subject: Re: 3D reconstruction of multiple, fluorescently labelled, sections
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi Emma,
>
> Have you seen the work from Stephen Smith's Lab at Stanford with array tomography? This is a link to a Cold Spring Harbor Protocol.
>
> http :// cshprotocols . cshlp .org/content/2010/11/ pdb .top89.full
>
> Good luck,
> Louie
>
> ----- Original Message -----
> From: "Emma King" < emma .[hidden email]>
> To: CONFOCALMICROSCOPY @LISTS. UMN . EDU
> Sent: Friday, November 18, 2011 9:39:57 AM
> Subject: 3D reconstruction of multiple, fluorescently labelled , sections
>
> *****
> To join, leave or search the confocal microscopy listserv , go to:
> http ://lists. umn . edu /cgi-bin/ wa ?A0= confocalmicroscopy
> *****
>
> We would like to take serial sections (20 microns thick) of rat spinal
> cord (up to 1cm long), label them with a bright and specific fluorescent
> label, acquire images (we can use either a widefield or confocal
> microscope) and then reconstruct the data in to one, 3D structure.
>
> We have the sectioning, staining and acquisition parameters/options
> under control, but don't have any software capable of reconstructing
> the resultant images. Does anyone have any suggestions as to what
> software to use and where to get it from?
>
> Any help much appreciated.
>
> Cheers,
> Emma
>
> Advanced Microscopy Unit
> School of Biomedical Sciences
> Univeristy of Nottingham
>
>
> --
>
>
>
> Louis Kerr
> lkerr @ mbl . edu
>
> Research and Education Support Coordinator
> Marine Biological Laboratory
> 7 MBL Street
> Woods Hole, MA 02543
> 508-289-7273
> 508-540-6902 (FAX)
> 508-292-0289 (Cell phone)
>
> VISIT OUR WEB SITES:
> www . mbl . edu
> www .courses. mbl . edu
>
> ------------------------------
>
> Date:    Fri, 18 Nov 2011 16:51:30 +0100
> From:    Tineke Vendrig <[hidden email]>
> Subject: Re: 3D reconstruction of multiple, fluorescently labelled, sections
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> We use the Andor software for our 3D movies, works nice and good!
>
> Tineke Vendrig
>
> --
> Tineke Vendrig, ing
> technical engineer optical microscopy
> Delft University of Technology
> Bionano Science
> Kavli Institute of Nanoscience
> Lorentzweg 1
> 2628LJ Delft
> room F185
> Tel: [phone]
> Fax:[phone]
> email: [hidden email]
> mobile phone: [phone]
>
>
> 2011/11/18 Emma King <[hidden email]>
>
>> *****
>> To join, leave or search the confocal microscopy listserv, go to:
>> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>> *****
>>
>> We would like to take serial sections (20 microns thick) of rat spinal
>> cord (up to 1cm long), label them with a bright and specific fluorescent
>> label, acquire images (we can use either a widefield or confocal
>> microscope) and then reconstruct the data in to one, 3D structure.
>>
>> We have the sectioning, staining and acquisition parameters/options
>> under control, but don't have any software capable of reconstructing
>> the resultant images. Does anyone have any suggestions as to what
>> software to use and where to get it from?
>>
>> Any help much appreciated.
>>
>> Cheers,
>> Emma
>>
>> Advanced Microscopy Unit
>> School of Biomedical Sciences
>> Univeristy of Nottingham
>>
>
> ------------------------------
>
> Date:    Fri, 18 Nov 2011 12:28:12 -0500
> From:    "Cammer, Michael" <[hidden email]>
> Subject: Olympus Corp in financial trouble?
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=3Dconfocalmicroscopy
> *****
>
> "Japanese officials say that at least $4.9 billion is unaccounted for in a =
> financial scandal at Olympus<http://topics.nytimes.com/top/news/business/co=
> mpanies/olympus_corporation/index.html?inline=3Dnyt-org> and are investigat=
> ing whether much of that money went to companies with links to organized cr=
> ime."
> http://www.nytimes.com/2011/11/18/business/global/japanese-police-investiga=
> te-olympus.html?_r=3D1&scp=3D3&sq=3Dolympus&st=3Dcse
>
>
> ________________________________________________________
> Michael Cammer, Assistant Research Scientist
> Skirball Institute of Biomolecular Medicine
> Lab: [phone]  Cell: [phone]
>
> </PRE>
> <html>
> <body>
> ------------------------------------------------------------<br />
> This email message, including any attachments, is for the sole use of the i=
> ntended recipient(s) and may contain information that is proprietary, confi=
> dential, and exempt from disclosure under applicable law. Any unauthorized =
> review, use, disclosure, or distribution is prohibited. If you have receive=
> d this email in error please notify the sender by return email and delete t=
> he original message. Please note, the recipient should check this email and=
> any attachments for the presence of viruses. The organization accepts no l=
> iability for any damage caused by any virus transmitted by this email.<br />
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
> =3D=3D=3D=3D=3D=3D=3D=3D
> </body>
> </html>
> <PRE>
>
> ------------------------------
>
> Date:    Fri, 18 Nov 2011 12:18:55 -0600
> From:    Johannes Schindelin <[hidden email]>
> Subject: Re: RE 3D reconstruction of multiple, fluorescently labelled, sections
>
>  This message is in MIME format.  The first part should be readable text,
>  while the remaining parts are likely unreadable without MIME-aware tools.
>
> --Boundary_(ID_BmV8ySyi3ZWYFpVvpZWp+A)
> Content-type: TEXT/PLAIN; charset=ISO-8859-15
> Content-transfer-encoding: 8BIT
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> On Fri, 18 Nov 2011, [hidden email] wrote:
>
>> Emma King <[hidden email]>@LISTS.UMN.EDU
>> Envoyé par : Confocal Microscopy List <[hidden email]>
>> 2011-11-18 09:39
>>
>>> We would like to take serial sections (20 microns thick) of rat spinal
>>> cord (up to 1cm long), label them with a bright and specific
>>> fluorescent label, acquire images (we can use either a widefield or
>>> confocal microscope) and then reconstruct the data in to one, 3D
>>> structure.
>>
>>> We have the sectioning, staining and acquisition parameters/options
>>> under control, but don't have any software capable of reconstructing
>>> the resultant images. Does anyone have any suggestions as to what
>>> software to use and where to get it from?
>>
>> In fact you want to add mutltiple Z-series together in order to form one
>> huge serie.  First, you will need a good computer and 2nd, I have done
>> it using Huygens software (SVI).
>>
>> Also, I am pretty sure that there is a plugin In" Image J" that can do
>> that.  Do not forget to do that with a good computer!!!!
>
> If all you want to do is a volume rendering, there are indeed 2 ImageJ
> plugins to do the job: Volume Viewer (non-accelerated) and 3D Viewer (this
> one uses your graphics adapter's accelerated 3D rendering).
>
> However, if you need to have surface models, you might want to look into
> the TrakEM2 plugin. It is very powerful, therefore it takes some training
> before one can exploit its capabilities in full.
>
> If you do not want to bother to find all the bits and pieces required for
> these plugins to run, please feel free to download Fiji (http://fiji.sc/)
> which bundles ImageJ with a lot of plugins (including the 3 mentioned
> above).
>
> Ciao,
> Johannes
>
> --Boundary_(ID_BmV8ySyi3ZWYFpVvpZWp+A)--
>
> ------------------------------
>
> Date:    Fri, 18 Nov 2011 11:02:21 -0800
> From:    "Armstrong, Brian" <[hidden email]>
> Subject: Re: RE 3D reconstruction of multiple, fluorescently labelled, sections
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=3Dconfocalmicroscopy
> *****
>
> You could try Reconstruct from NIH Human Brain project =
> (http://synapses.clm.utexas.edu/tools/reconstruct/reconstruct.stm ).
>
> In my opinion, Amira, Imaris, and Volocity, are probably best at 3D =
> visualization tools.=20
>
> Cheers,
>
> Brian D Armstrong PhD
> Assistant Research Professor
> Light Microscopy Core=20
> Beckman Research Institute
> City of Hope
> Dept of Neuroscience
> 1450 E Duarte Rd
> Duarte, CA 91010
> 626-256-4673 x62872
>
> http://www.cityofhope.org/research/support/Light-Microscopy-Digital-Imaging=
> /Pages/default.aspx
>
>
> -----Original Message-----
> =46rom: Confocal Microscopy List [mailto:[hidden email]] =
> =
> On Behalf Of Johannes Schindelin
> Sent: Friday, November 18, 2011 10:19 AM
> To: [hidden email]
> Subject: Re: RE 3D reconstruction of multiple, fluorescently labelled, =
> sections
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa=3FA0=3Dconfocalmicroscopy
> *****
>
> On Fri, 18 Nov 2011, [hidden email] wrote:
>
>> Emma King <[hidden email]>@LISTS.UMN.EDU=20
>> Envoy=E9 par : Confocal Microscopy List <[hidden email]>
>> 2011-11-18 09:39
>>
>>> We would like to take serial sections (20 microns thick) of rat spinal
>>> cord (up to 1cm long), label them with a bright and specific
>>> fluorescent label, acquire images (we can use either a widefield or
>>> confocal microscope) and then reconstruct the data in to one, 3D
>>> structure.=20
>> =20
>>> We have the sectioning, staining and acquisition parameters/options
>>> under control, but don't have any software capable of reconstructing
>>> the resultant images. Does anyone have any suggestions as to what
>>> software to use and where to get it from=3F=20
>> =20
>> In fact you want to add mutltiple Z-series together in order to form one
>> huge serie.  First, you will need a good computer and 2nd, I have done
>> it using Huygens software (SVI).=20
>>
>> Also, I am pretty sure that there is a plugin In" Image J" that can do=20
>> that.  Do not forget to do that with a good computer!!!!
>
> If all you want to do is a volume rendering, there are indeed 2 ImageJ
> plugins to do the job: Volume Viewer (non-accelerated) and 3D Viewer (this
> one uses your graphics adapter's accelerated 3D rendering).
>
> However, if you need to have surface models, you might want to look into
> the TrakEM2 plugin. It is very powerful, therefore it takes some training
> before one can exploit its capabilities in full.
>
> If you do not want to bother to find all the bits and pieces required for
> these plugins to run, please feel free to download Fiji (http://fiji.sc/)
> which bundles ImageJ with a lot of plugins (including the 3 mentioned
> above).
>
> Ciao,
> Johannes
>
>
> ---------------------------------------------------------------------
> *SECURITY/CONFIDENTIALITY WARNING: =20
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>
> ---------------------------------------------------------------------
>
> ------------------------------
>
> Date:    Fri, 18 Nov 2011 13:24:11 -0600
> From:    Martin Wessendorf <[hidden email]>
> Subject: Re: Olympus Corp in financial trouble?
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Michael et al--
>
> On 11/18/2011 11:28 AM, Cammer, Michael wrote:
>
>> "Japanese officials say that at least $4.9 billion is unaccounted for in a financial scandal at Olympus<http://topics.nytimes.com/top/news/business/companies/olympus_corporation/index.html?inline=nyt-org>  and are investigating whether much of that money went to companies with links to organized crime."
>> http://www.nytimes.com/2011/11/18/business/global/japanese-police-investigate-olympus.html?_r=1&scp=3&sq=olympus&st=cse
>
> I've seen these reports, too, over the past few weeks.  However,
> although it seems quite likely that their stockholders will be unhappy
> with them, it's unclear (to me, at least!) that the company is in
> financial trouble yet.
>
> Disclaimer: I'm definitely not a certified financial advisor!
>
> Martin Wessendorf
> --
> Martin Wessendorf, Ph.D.                   office: [phone]
> Assoc Prof, Dept Neuroscience                 lab: [phone]
> University of Minnesota             Preferred FAX: [phone]
> 6-145 Jackson Hall, 321 Church St. SE    Dept Fax: [phone]
> Minneapolis, MN  55455                    e-mail: [hidden email]
>
> ------------------------------
>
> Date:    Fri, 18 Nov 2011 15:26:43 -0600
> From:    Martin Wessendorf <[hidden email]>
> Subject: (lots) more on Olympus
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> For anyone who's interested:
>
> http://newsfeedresearcher.com/data/articles_b47/olympus-woodford-company.html
>
> Martin
> --
> Martin Wessendorf, Ph.D.                   office: [phone]
> Assoc Prof, Dept Neuroscience                 lab: [phone]
> University of Minnesota             Preferred FAX: [phone]
> 6-145 Jackson Hall, 321 Church St. SE    Dept Fax: [phone]
> Minneapolis, MN  55455                    e-mail: [hidden email]
>
> ------------------------------
>
> Date:    Fri, 18 Nov 2011 14:34:04 -0800
> From:    Iain Johnson <[hidden email]>
> Subject: Re: Cell viability assay
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Calcein AM  (intracellular esterase substrate).  Incubate cells for 10
> minutes in 1 microM calcein AM in serum-free medium at 37C.  Wash off
> staining medium and replace with complete culture medium.  Image in
> FITC/GFP channel.
>
> You can also add a second dimension to the assay (at the expense of giving
> up more spectral real estate).
>
> SYTOX Orange (Molecular Probes; membrane permeability probe).  Add to
> complete culture medium at 5 microM.  Do not wash.  Image in TRITC/Cy3
> channel.
>
> Iain
>
> Iain Johnson Consulting
> Eugene, OR
> [phone]
>
> On Thu, Nov 17, 2011 at 7:23 AM, B. Prabhakar Pandian <[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>
>> *****
>>
>> Hello,
>>            I am emailing to see if anybody has a suggestion for a cell
>> viability/toxicity assay that works similar to LDH/Caspase but relies on
>> internal enzymes rather than in the supernatant.  In addition, it should be
>> compatible with fluorescence microscope.
>>
>> Thanks,
>>
>> -Prabhakar
>>
>
> ------------------------------
>
> Date:    Fri, 18 Nov 2011 19:50:53 -0500
> From:    Christian Wilms <[hidden email]>
> Subject: Re: Fast two-photon imaging: Constant fraction discriminator and variable delay for Laser pulse-synch
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Regarding the delay: if you do not need it to flexible in timing,
> simply getting a coaxial cable of the correct length (20 cm
> corresponds roughly to 1 ns) is one option. A bit more flexible and
> still affordable are variable delay lines such as the Ortec 425 <http://www.ortec-online.com/download/425A.pdf
>
> Best, Christian
>
> ------------------------------
>
> Date:    Fri, 18 Nov 2011 23:08:24 -0500
> From:    "Alison J. North" <[hidden email]>
> Subject: Re: Olympus Corp in financial trouble? We certainly hope not!
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=3Dconfocalmicroscopy
> *****
>
> Hey Michael,
>
> There is no question that Olympus has been going through hell this year - s=
> tarting with the tsunami, and who could have guessed that things could have=
> got even worse because of a few crooks (worst case) or idiots (best case) =
> at the top....   Given that we own several high-end Olympus microscopes, we=
> obviously have a vested interest in the company staying afloat and are und=
> erstandably all concerned.  More than that though, I have worked with the s=
> ame Olympus team for over 11 years now and they have not only proved to be =
> great colleagues but also good friends - we have caught wild mice on our ha=
> nds and knees in my lab together, I have played despicable April Fool's jok=
> es on them (well truthfully, only once - they have refused to visit my lab =
> on April 1st ever since), and they have proved themselves such wizards at s=
> olving the most mysterious and intractable microscope problems that we nick=
> named the two local guys Dumbledore and Gandalf.  At this point I think any=
> discussion of what will happen is just pointless speculation, and one whic=
> h they cannot possibly enter into, so the best we can do is to trust this w=
> ill all blow over eventually and offer the microscope guys our support, say=
> ing: we're rooting for you, and here's to 2012 being a far better year for =
> you than 2011!
>
> Best,
> Alison
> P.S.  Sorry if I'm gushing to the confocal listserver - blame the glass of =
> wine in my hand and the fact that I just came back from the movies :-).=20
>
>  =20
> ________________________________________
> From: Confocal Microscopy List [[hidden email]] On Behalf=
> Of Cammer, Michael [[hidden email]]
> Sent: Friday, November 18, 2011 12:28 PM
> To: [hidden email]
> Subject: Olympus Corp in financial trouble?
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=3Dconfocalmicroscopy
> *****
>
> "Japanese officials say that at least $4.9 billion is unaccounted for in a =
> financial scandal at Olympus<http://topics.nytimes.com/top/news/business/co=
> mpanies/olympus_corporation/index.html?inline=3Dnyt-org> and are investigat=
> ing whether much of that money went to companies with links to organized cr=
> ime."
> http://www.nytimes.com/2011/11/18/business/global/japanese-police-investiga=
> te-olympus.html?_r=3D1&scp=3D3&sq=3Dolympus&st=3Dcse
>
>
> ________________________________________________________
> Michael Cammer, Assistant Research Scientist
> Skirball Institute of Biomolecular Medicine
> Lab: [phone]  Cell: [phone]
>
> </PRE>
> <html>
> <body>
> ------------------------------------------------------------<br />
> This email message, including any attachments, is for the sole use of the i=
> ntended recipient(s) and may contain information that is proprietary, confi=
> dential, and exempt from disclosure under applicable law. Any unauthorized =
> review, use, disclosure, or distribution is prohibited. If you have receive=
> d this email in error please notify the sender by return email and delete t=
> he original message. Please note, the recipient should check this email and=
> any attachments for the presence of viruses. The organization accepts no l=
> iability for any damage caused by any virus transmitted by this email.<br /=
>>
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
> =3D=3D=3D=3D=3D=3D=3D=3D
> </body>
> </html>
> <PRE>
>
> ------------------------------
>
> End of CONFOCALMICROSCOPY Digest - 17 Nov 2011 to 18 Nov 2011 (#2011-88)
> ************************************************************************
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[Ford,Jason R.]

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

Has anyone using the MacOSX Snow Leopard (10.6.x) had any issues with
playing uncompressed .avi files in QuickTime (either QuickTimeX Player or
QuickTime 7.6.6 for 10.6.x)?

My movies play fine on a machine with OSX 10.5.8 using QT 7.7, but they
won¹t play on a newer machine using OSX 10.6.8 and QT 7.6.6 (you can¹t
install QT 7.7 with OSX 10.6.8); addition of various codecs and readers
(DivX, Xvid, Flip4Mac, Perian, 3ivx) does not help. Specifically, these are
.avi movies processed in UltraView or MatLab that worked fine on my previous
Apple machine but will not run on my newer machine running OSX 10.6.8.

The movies play in VLC regardless of the platform, but VLC movies can¹t be
embedded into PowerPoint 2008 or 2011 (as far as I know) and must be played
externally; if someone knows how to tell PowerPoint to use VLC instead of
QT, then I would be most interested to know.

Any insight into potential problems experienced by others would be most
helpful for troubleshooting this issue.

Thanks,

Jason Ford

[Johannes Schindelin]

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

Hi,

On Mon, 21 Nov 2011, Tim Feinstein wrote:

> This recent paper in Traffic describes a new ImageJ tool that could
> provide what you need:
>
> http://onlinelibrary.wiley.com/doi/10.1111/j.1600-0854.2011.01309.x/abstract

The software seems to be offered here:

        http://www.rappoportlab.com/auto-align1

Unfortunately, it is not open for improvement.

Ciao,
Johannes

[John Oreopoulos]

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

Hi Jason,

Your posting reminded me of a similar problem I described back in July of 2007 on the ImageJ listserver:

https://list.nih.gov/cgi-bin/wa.exe?A2=ind0707&L=IMAGEJ&D=0&P=45684

You can see in that thread that a few people suggested a few solutions back then, but in the end, the problem seemed to fix itself after updating quicktime (at least on my laptop) almost a year later:

http://imagej.588099.n2.nabble.com/Re-problem-opening-avi-files-created-by-ImageJ-in-quicktime-after-upgrading-to-imovie-HD-6-td636404.html

It was one of those mysteries I couldn't quite figure out. Wish I could give you more help than that. Not my field of expertise.

John Oreopoulos


On 2011-11-21, at 11:14 AM, Ford,Jason R. wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Has anyone using the MacOSX Snow Leopard (10.6.x) had any issues with
> playing uncompressed .avi files in QuickTime (either QuickTimeX Player or
> QuickTime 7.6.6 for 10.6.x)?
>
> My movies play fine on a machine with OSX 10.5.8 using QT 7.7, but they
> won’t play on a newer machine using OSX 10.6.8 and QT 7.6.6 (you can’t
> install QT 7.7 with OSX 10.6.8); addition of various codecs and readers
> (DivX, Xvid, Flip4Mac, Perian, 3ivx) does not help. Specifically, these are
> .avi movies processed in UltraView or MatLab that worked fine on my previous
> Apple machine but will not run on my newer machine running OSX 10.6.8.
>
> The movies play in VLC regardless of the platform, but VLC movies can’t be
> embedded into PowerPoint 2008 or 2011 (as far as I know) and must be played
> externally; if someone knows how to tell PowerPoint to use VLC instead of
> QT, then I would be most interested to know.
>
> Any insight into potential problems experienced by others would be most
> helpful for troubleshooting this issue.
>
> Thanks,
>
> Jason Ford

[Michael Schell]

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

I can report the mirror image of your problem.  When I create .avi
movies (jpg compression or no compression) using ImageJ on a Mac running
Snow Leopard, these won't play in Powerpoint on a Mac running 10.5.8.
The incompatibility appears only when the movies are inserted into
Powerpoint.   ImageJ on the 10.5.8 machine can read them.   The
workaround is to open them in ImageJ on the 10.5.8 machine and re-save
as .mov files for Quicktime.  These play in Powerpoint on 10.5.8 but not
on Snow Leopard.  As usual, the end users are the victims of the codec
wars--and Powerpoint always makes the problems worse.


 Michael
 
Michael J. Schell, Ph.D., CIV, USUHS
Assist. Professor
Dept. of Pharmacology
Uniformed Services University
4301 Jones Bridge Rd.
Bethesda, MD  20814-3220
tel:  [phone]
[hidden email]
>>> "Ford,Jason R."  11/21/11 3:38 PM >>>
*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Has anyone using the MacOSX Snow Leopard (10.6.x) had any issues with
playing uncompressed .avi files in QuickTime (either QuickTimeX Player
or
QuickTime 7.6.6 for 10.6.x)?

My movies play fine on a machine with OSX 10.5.8 using QT 7.7, but they
won¹t play on a newer machine using OSX 10.6.8 and QT 7.6.6 (you can¹t
install QT 7.7 with OSX 10.6.8); addition of various codecs and readers
(DivX, Xvid, Flip4Mac, Perian, 3ivx) does not help. Specifically, these
are
.avi movies processed in UltraView or MatLab that worked fine on my
previous
Apple machine but will not run on my newer machine running OSX 10.6.8.

The movies play in VLC regardless of the platform, but VLC movies can¹t
be
embedded into PowerPoint 2008 or 2011 (as far as I know) and must be
played
externally; if someone knows how to tell PowerPoint to use VLC instead
of
QT, then I would be most interested to know.

Any insight into potential problems experienced by others would be most
helpful for troubleshooting this issue.

Thanks,

Jason Ford


Classification:  UNCLASSIFIED
Caveats: None


Classification:  UNCLASSIFIED
Caveats: None

[Dmitry Sokolov]

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

Hi Jason and Michael,

movie converter could be another option like Any Video Converter for PC. Mac World should have even better solution, by definition.

Please share you experience at MIAWiki knowledge node on the subject:
  http://confocal-manawatu.pbworks.com/w/page/16347023/Movie%20converters
for your quicker reference in future.

With kind regards,
Dmitry
MIAWiki for Mass Collaboration
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Dr. Dmitry Sokolov
*LYNX Analytics: * Image Analysis - Data Processing - Knowledge Transfer
/Scanning Confocal / Atomic Force Microscopy & Spectroscopy/
Mob: [phone]

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


On 22/11/2011 10:00 a.m., Michael Schell wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> I can report the mirror image of your problem.  When I create .avi
> movies (jpg compression or no compression) using ImageJ on a Mac running
> Snow Leopard, these won't play in Powerpoint on a Mac running 10.5.8.
> The incompatibility appears only when the movies are inserted into
> Powerpoint.   ImageJ on the 10.5.8 machine can read them.   The
> workaround is to open them in ImageJ on the 10.5.8 machine and re-save
> as .mov files for Quicktime.  These play in Powerpoint on 10.5.8 but not
> on Snow Leopard.  As usual, the end users are the victims of the codec
> wars--and Powerpoint always makes the problems worse.
>
>
>   Michael
>
> Michael J. Schell, Ph.D., CIV, USUHS
> Assist. Professor
> Dept. of Pharmacology
> Uniformed Services University
> 4301 Jones Bridge Rd.
> Bethesda, MD  20814-3220
> tel:  [phone]
> [hidden email]
>>>> "Ford,Jason R."  11/21/11 3:38 PM>>>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Has anyone using the MacOSX Snow Leopard (10.6.x) had any issues with
> playing uncompressed .avi files in QuickTime (either QuickTimeX Player
> or
> QuickTime 7.6.6 for 10.6.x)?
>
> My movies play fine on a machine with OSX 10.5.8 using QT 7.7, but they
> won¹t play on a newer machine using OSX 10.6.8 and QT 7.6.6 (you can¹t
> install QT 7.7 with OSX 10.6.8); addition of various codecs and readers
> (DivX, Xvid, Flip4Mac, Perian, 3ivx) does not help. Specifically, these
> are
> .avi movies processed in UltraView or MatLab that worked fine on my
> previous
> Apple machine but will not run on my newer machine running OSX 10.6.8.
>
> The movies play in VLC regardless of the platform, but VLC movies can¹t
> be
> embedded into PowerPoint 2008 or 2011 (as far as I know) and must be
> played
> externally; if someone knows how to tell PowerPoint to use VLC instead
> of
> QT, then I would be most interested to know.
>
> Any insight into potential problems experienced by others would be most
> helpful for troubleshooting this issue.
>
> Thanks,
>
> Jason Ford
>
>
> Classification:  UNCLASSIFIED
> Caveats: None
>
>
> Classification:  UNCLASSIFIED
> Caveats: None
>
>

[Keith Morris]

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

I tend to be going the other way, but I always convert *.avi or time-lapses movies to *.mov when shifting to Macs, as Apple has a pathological hatred of anything it can't charge a 30% levy for on iTunes.  As avi is the Microsoft Windows format it will never be Apple Mac friendly. I always use QuickTime Pro [cost about £20 to upgrade over freebie Quicktime] for this sort of thing as it runs on Apples or PCs and being an Apple product it is Mac friendly and easy to use [as it's so basic], but it does the job. Likewise now-a-days you need to convert a Mac's *.mov video to *.avi to run it imbedded within a Windows PowerPoint presentation, whereas in the olden days Windows Office was allowed to run *.mov files.

Regards

Keith

---------------------------------------------------------------------------
Dr Keith J. Morris,
Molecular Cytogenetics and Microscopy Core,
Laboratory 00/069 and 00/070,
The Wellcome Trust Centre for Human Genetics,
Roosevelt Drive,
Oxford  OX3 7BN,
United Kingdom.

Telephone:  [phone]
Email:  [hidden email]
Web-pages: http://www.well.ox.ac.uk/molecular-cytogenetics-and-microscopy

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Dmitry Sokolov
Sent: 21 November 2011 21:44
To: [hidden email]
Subject: Re: .avi problems in Mac OSX 10.6.x

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

Hi Jason and Michael,

movie converter could be another option like Any Video Converter for PC. Mac World should have even better solution, by definition.

Please share you experience at MIAWiki knowledge node on the subject:
  http://confocal-manawatu.pbworks.com/w/page/16347023/Movie%20converters
for your quicker reference in future.

With kind regards,
Dmitry
MIAWiki for Mass Collaboration
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Dr. Dmitry Sokolov
*LYNX Analytics: * Image Analysis - Data Processing - Knowledge Transfer
/Scanning Confocal / Atomic Force Microscopy & Spectroscopy/
Mob: [phone]

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


On 22/11/2011 10:00 a.m., Michael Schell wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> I can report the mirror image of your problem.  When I create .avi
> movies (jpg compression or no compression) using ImageJ on a Mac running
> Snow Leopard, these won't play in Powerpoint on a Mac running 10.5.8.
> The incompatibility appears only when the movies are inserted into
> Powerpoint.   ImageJ on the 10.5.8 machine can read them.   The
> workaround is to open them in ImageJ on the 10.5.8 machine and re-save
> as .mov files for Quicktime.  These play in Powerpoint on 10.5.8 but not
> on Snow Leopard.  As usual, the end users are the victims of the codec
> wars--and Powerpoint always makes the problems worse.
>
>
>   Michael
>
> Michael J. Schell, Ph.D., CIV, USUHS
> Assist. Professor
> Dept. of Pharmacology
> Uniformed Services University
> 4301 Jones Bridge Rd.
> Bethesda, MD  20814-3220
> tel:  [phone]
> [hidden email]
>>>> "Ford,Jason R."  11/21/11 3:38 PM>>>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Has anyone using the MacOSX Snow Leopard (10.6.x) had any issues with
> playing uncompressed .avi files in QuickTime (either QuickTimeX Player
> or
> QuickTime 7.6.6 for 10.6.x)?
>
> My movies play fine on a machine with OSX 10.5.8 using QT 7.7, but they
> won¹t play on a newer machine using OSX 10.6.8 and QT 7.6.6 (you can¹t
> install QT 7.7 with OSX 10.6.8); addition of various codecs and readers
> (DivX, Xvid, Flip4Mac, Perian, 3ivx) does not help. Specifically, these
> are
> .avi movies processed in UltraView or MatLab that worked fine on my
> previous
> Apple machine but will not run on my newer machine running OSX 10.6.8.
>
> The movies play in VLC regardless of the platform, but VLC movies can¹t
> be
> embedded into PowerPoint 2008 or 2011 (as far as I know) and must be
> played
> externally; if someone knows how to tell PowerPoint to use VLC instead
> of
> QT, then I would be most interested to know.
>
> Any insight into potential problems experienced by others would be most
> helpful for troubleshooting this issue.
>
> Thanks,
>
> Jason Ford
>
>
> Classification:  UNCLASSIFIED
> Caveats: None
>
>
> Classification:  UNCLASSIFIED
> Caveats: None
>
>

[Steve Baxter-2]

Hi Jason,

I'm not sure if you're using Volocity or ImageSuite to control your UltraVIEW, but assuming it's Volocity here's some general advice that I hope might be useful!

- On Windows, I would prefer WMV over AVI - WMV is a newer format with better compression and support. It also has much less to configure (and therefore much less to go wrong).

- On Mac OS X, I would prefer Quicktime with H.264 compression. This is a modern, high-quality codec.

If you're using Powerpoint, then the situation is somewhat harder:

- If you're using Volocity on Windows and PowerPoint for Windows then export as WMV. This should work out of the box.

- If you're using Volocity on Mac OS X and PowerPoint for Mac OS X then export as Quicktime with H.264 compression. This should also work.

- If you're using Volocity on Windows and PowerPoint for Mac OS X then export as WMV and install "Flip4Mac" on Mac OS X. This is free and will allow Quicktime to play WMV files.

- If you're using Volocity on Mac OS X and PowerPoint for Windows then it's a bit more tricky - PowerPoint for Windows is (frustratingly) not compatible with Quicktime. The best solution I have found is to convert the movie to WMV on Windows, there are lots of free applications for this, or you can use this rather nifty website (no commercial interest):

http://video.online-convert.com/convert-to-wmv

Cheers,

Steve

________________________________

Steve Baxter | R&D Director, Scientific Imaging Software

PerkinElmer | For the Better

[hidden email]

Phone:  [phone]

Viscount Centre 2, Millburn Hill Rd, Coventry, CV4 7HS, UK

www.perkinelmer.com

________________________________

Please consider the environment before printing this e-mail.

This e-mail message and any attachments are confidential and proprietary to PerkinElmer, Inc.  If you are not the intended recipient of this message, please inform the sender by replying to this email or sending a message to the sender and destroy the message and any attachments.  Thank you.

From: "Ford,Jason R." <[hidden email]<mailto:[hidden email]>>
Reply-To: Confocal Microscopy List <[hidden email]<mailto:[hidden email]>>
Date: Mon, 21 Nov 2011 10:14:44 -0600
To: <[hidden email]<mailto:[hidden email]>>
Subject: [CONFOCALMICROSCOPY] .avi problems in Mac OSX 10.6.x

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

Has anyone using the MacOSX Snow Leopard (10.6.x) had any issues with
playing uncompressed .avi files in QuickTime (either QuickTimeX Player or
QuickTime 7.6.6 for 10.6.x)?

My movies play fine on a machine with OSX 10.5.8 using QT 7.7, but they
won¹t play on a newer machine using OSX 10.6.8 and QT 7.6.6 (you can¹t
install QT 7.7 with OSX 10.6.8); addition of various codecs and readers
(DivX, Xvid, Flip4Mac, Perian, 3ivx) does not help. Specifically, these are
.avi movies processed in UltraView or MatLab that worked fine on my previous
Apple machine but will not run on my newer machine running OSX 10.6.8.

The movies play in VLC regardless of the platform, but VLC movies can¹t be
embedded into PowerPoint 2008 or 2011 (as far as I know) and must be played
externally; if someone knows how to tell PowerPoint to use VLC instead of
QT, then I would be most interested to know.

Any insight into potential problems experienced by others would be most
helpful for troubleshooting this issue.

Thanks,

Jason Ford

[Justin Ross]

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

Hi,
I had a similar problem recently with avi files made by matlab and FIJI that I wanted to play in powerpoint. Provided you have the correct codecs for the avi, I found that changing the file extension from .avi to .mpg made it play properly in powerpoint regardless of the codec used to encode it.

Hope this helps,
Justin.

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Baxter, Steve
Sent: Tuesday, 22 November 2011 9:44 PM
To: [hidden email]
Subject: Re: .avi problems in Mac OSX 10.6.x

Hi Jason,

I'm not sure if you're using Volocity or ImageSuite to control your UltraVIEW, but assuming it's Volocity here's some general advice that I hope might be useful!

- On Windows, I would prefer WMV over AVI - WMV is a newer format with better compression and support. It also has much less to configure (and therefore much less to go wrong).

- On Mac OS X, I would prefer Quicktime with H.264 compression. This is a modern, high-quality codec.

If you're using Powerpoint, then the situation is somewhat harder:

- If you're using Volocity on Windows and PowerPoint for Windows then export as WMV. This should work out of the box.

- If you're using Volocity on Mac OS X and PowerPoint for Mac OS X then export as Quicktime with H.264 compression. This should also work.

- If you're using Volocity on Windows and PowerPoint for Mac OS X then export as WMV and install "Flip4Mac" on Mac OS X. This is free and will allow Quicktime to play WMV files.

- If you're using Volocity on Mac OS X and PowerPoint for Windows then it's a bit more tricky - PowerPoint for Windows is (frustratingly) not compatible with Quicktime. The best solution I have found is to convert the movie to WMV on Windows, there are lots of free applications for this, or you can use this rather nifty website (no commercial interest):

http://video.online-convert.com/convert-to-wmv

Cheers,

Steve

________________________________

Steve Baxter | R&D Director, Scientific Imaging Software

PerkinElmer | For the Better

[hidden email]

Phone:  [phone]

Viscount Centre 2, Millburn Hill Rd, Coventry, CV4 7HS, UK

www.perkinelmer.com

________________________________

Please consider the environment before printing this e-mail.

This e-mail message and any attachments are confidential and proprietary to PerkinElmer, Inc.  If you are not the intended recipient of this message, please inform the sender by replying to this email or sending a message to the sender and destroy the message and any attachments.  Thank you.

From: "Ford,Jason R." <[hidden email]<mailto:[hidden email]>>
Reply-To: Confocal Microscopy List <[hidden email]<mailto:[hidden email]>>
Date: Mon, 21 Nov 2011 10:14:44 -0600
To: <[hidden email]<mailto:[hidden email]>>
Subject: [CONFOCALMICROSCOPY] .avi problems in Mac OSX 10.6.x

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

Has anyone using the MacOSX Snow Leopard (10.6.x) had any issues with
playing uncompressed .avi files in QuickTime (either QuickTimeX Player or
QuickTime 7.6.6 for 10.6.x)?

My movies play fine on a machine with OSX 10.5.8 using QT 7.7, but they
won¹t play on a newer machine using OSX 10.6.8 and QT 7.6.6 (you can¹t
install QT 7.7 with OSX 10.6.8); addition of various codecs and readers
(DivX, Xvid, Flip4Mac, Perian, 3ivx) does not help. Specifically, these are
.avi movies processed in UltraView or MatLab that worked fine on my previous
Apple machine but will not run on my newer machine running OSX 10.6.8.

The movies play in VLC regardless of the platform, but VLC movies can¹t be
embedded into PowerPoint 2008 or 2011 (as far as I know) and must be played
externally; if someone knows how to tell PowerPoint to use VLC instead of
QT, then I would be most interested to know.

Any insight into potential problems experienced by others would be most
helpful for troubleshooting this issue.

Thanks,

Jason Ford

[Peter Werner]

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

If I had to take a wild guess, it sounds to me like a codec problem. That is,
either a folder that contains the codec you need to play the video was either
overwritten or moved, which is a common problem when you do a software
upgrade or re-install. If you've saved an old version of your system files, the
correct codec should still be there.

I also use a Mac and use VLC as my main video player alongside Quicktime,
and find it quite useful. I would recommend opening the video in VLC,
highlighting the video in the navigator window, and choosing "Get Info" from
the menu. This should tell you what kind of video you have (it might be an
abbreviation that you'll have to google), then do a search of your system to
see if you have the right codec. If not, you can often track down a Mac
installer for the codec.

Hope this helps,
Peter