I.T. questions

[Daniel James White]

Hi all,

Does anyone have a good solution for
having windows use a log in server (LDAP or similar)
for users to log into microscope system windows machines,
which also logs their usage (who - from when to when).

Some microscope software is tricky to get running properly on a
normal user account, as the manufacturers sometimes think its OK
to always have the admin user running the software.
That is clearly a very bad thing in a multi user environment.

Anyone have any experience there they want to share?

I am looking for something that works for windows XP and vista, and 32  
and 64 bit.
I have tried pGina on offline workstations, but didnt get very far die  
to 32 bit only for one of the plugins i needed.



cheers


Dan



Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

[phone] (German Mobile)
+49  (0)351 210 2627 (Work phone at MPI-CBG)
+49  (0)351 210 1078 (Fax MPI-CBG LMF)

http://www.bioimagexd.net  BioImageXD
http://pacific.mpi-cbg.de Fiji Fiji is just ImageJ - Batteries Included
http://www.chalkie.org.uk
[hidden email]
( [hidden email] )

[Mathieu Marchand-2]

Dear list,
Disclaimer: I am an IT person working on an imaging facility and am
familiar with the demands and common problems of data management
experienced by most facilities.

We always save images directly to our file server, even from fast
spinning disk systems with EMCCD camera. Our image acquisition
software can write directly to the server at up to 45MB/s (windows
client / samba server) or up to 90MB/s (linux client / NFS server).
This is just as fast (if not faster) than a local disk.
We only had a problem with Zeiss LSM software that introduced some
changes in version 4 and later that brakes saving on the network. We
are staying with LSM v3.2 that has no such problem and hope that they
will fix that.

We have multiple gigabit interfaces on the server and a gigabit
network isolated from the rest of the campus. But to achieve decent
speeds, the most important part is a good file server, as network
communications have a lot more overhead than local disks, leading to
often disappointing performance. I am personally very happy with our
36TB Sun X4500 server with the ZFS technology: it is really fast, it
has a lot of features (storage pooling, snapshots...), and is not too
expensive. A lot of other storage solutions can do the job, just keep
in mind that low cost (or even some middle range) solutions might not
perform fast enough (there is actually a reason why people spend
sometimes 5X more per GB for storage solutions). We are using the
central backup services of our institution. We are also working with
the OMERO solutions to index the data on the server. As OMERO is
getting better each release I have no doubt it will be working for us
in the near future.

We are using a central login system to allow all microscopes
workstations (linux and windows) to use the user accounts for login
and access personal space on the server. This is done by a samba
domain controller attached to a LDAP directory (you can also use
active directory). This is pretty much a standard IT solution. Our
user accounts and passwords are synchronized with our PPMS
(http://ppms.info) booking system (no IT administration needed to
create or modify users). Regular domain user accounts can be setup as
administrator when a (bad) imaging software requires that.

In my opinion if your institution cannot provide a proper IT solution
for your facility, you will need to hire an IT expert inside your
facility. I agree with other posts in the fact that even if you are
not officially responsible for your user's data storage and archiving,
your imaging facility is or will be one of the major generators of
data in your institution, and not having the proper infrastructure to
receive and archive that data could generate some serious bottlenecks
for your activity.
Mat

--
Mathieu Marchand
--
Bio-Imaging Resource Center, The Rockefeller University
1230 York Avenue, box 209, New York, NY 10065
http://www.rockefeller.edu/bioimaging




On Mon, Jul 13, 2009 at 3:55 AM, Daniel James White<[hidden email]> wrote:

> Hi all,
>
> Does anyone have a good solution for
> having windows use a log in server (LDAP or similar)
> for users to log into microscope system windows machines,
> which also logs their usage (who - from when to when).
>
> Some microscope software is tricky to get running properly on a
> normal user account, as the manufacturers sometimes think its OK
> to always have the admin user running the software.
> That is clearly a very bad thing in a multi user environment.
>
> Anyone have any experience there they want to share?
>
> I am looking for something that works for windows XP and vista, and 32 and
> 64 bit.
> I have tried pGina on offline workstations, but didnt get very far die to 32
> bit only for one of the plugins i needed.
>
>
>
> cheers
>
>
> Dan
>
>
>
> Dr. Daniel James White BSc. (Hons.) PhD
> Senior Microscopist / Image Visualisation, Processing and Analysis
> Light Microscopy and Image Processing Facilities
> Max Planck Institute of Molecular Cell Biology and Genetics
> Pfotenhauerstrasse 108
> 01307 DRESDEN
> Germany
>
> [phone] (German Mobile)
> +49  (0)351 210 2627 (Work phone at MPI-CBG)
> +49  (0)351 210 1078 (Fax MPI-CBG LMF)
>
> http://www.bioimagexd.net       BioImageXD
> http://pacific.mpi-cbg.de Fiji  Fiji is just ImageJ - Batteries Included
> http://www.chalkie.org.uk
> [hidden email]
> ( [hidden email] )
>

--

[Daniel James White]

On Jul 14, 2009, at 7:03 AM, CONFOCALMICROSCOPY automatic digest  
system wrote:

>
> Date:    Mon, 13 Jul 2009 20:34:47 +1000
> From:    Rosemary White <[hidden email]>
> Subject: Re: I.T. questions
>
> Ah, yes, in an ideal world some of this might happen, but it won't  
> happen
> here.  Our IT folk, as in many places, are in an understaffed and  
> overworked
> department.

Everyone is busy....Every department could use more people,
  the trick is to dangle attractive carrots that people will bite on.


>
> I don't think saving data to one place and copying to another is  
> such a big
> deal, the network is pretty fast.  At least you then have two copies  
> of the
> data.

In some ways thats a very good thing.
But whe happens when one version of the data is renamed
or processed or other wise modified?
There is no version control system to keep track of what happened to  
what and where it is...

but version control is a another huge issue that we mostly ignore....
but we should not. Its another meta data related problem in essence.

> Perhaps if we had really huge multi-TB sized data sets it'd be a
> problem, but not yet.  Our flakiest instruments can't be networked  
> anyway.

Pity thats the case. I guess when you get new stuff you will demand  
that it can be networked...?
As i mentioned earlier, it is not acceptable for manufacturers to  
charge big money for
instruments that are targeted at multi user environments but don't  
play nice on networks and dont like virus scanners.
The power lies in our hands there. we can vote with our funding.

>
> And compared to the months and years and people power it's taken to  
> develop
> and process the biological materials (plants in our case) to be  
> imaged, the
> time taken for imaging and data transfer is negligible.  The  
> subsequent
> image and statistical analysis also takes much longer than  
> collection of the
> original images.

I guess there is a point there, but surely,
the huge time and effort needed to make the samples
makes the image data even more precious?
So surely its worth looking after it as best is possible?


cheers

Dan

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

[phone] (German Mobile)
+49  (0)351 210 2627 (Work phone at MPI-CBG)
+49  (0)351 210 1078 (Fax MPI-CBG LMF)

http://www.bioimagexd.net  BioImageXD
http://pacific.mpi-cbg.de Fiji Fiji is just ImageJ - Batteries Included
http://www.chalkie.org.uk
[hidden email]
( [hidden email] )

[Cameron Nowell]

I am trying to segment out membrane, cytoplasm and nuclei from a
confocal image set. This is so we can measure translocation of a protein
from the membrane to the cytoplasm/nucleus over time. I can do this in
MetaMorph but would like to be able to do it in 3D in Imaris if
possible.

The sample is stained as follows
- Nuclei - DAPI
- Whole Cell - CellMask (Invitrogen)
- Protein of Interest (Alexa Antibody)

Since there is not a specific stain from membrane or cytoplasm i have
been doing the following
- Segment out whole cells and create a binary mask
- Erode that mask by 4 or so pixels, this represents the cytoplasm
and nuclei of the cell
- Subtract the eroded mask from the whole cell mask. This leave a
ring that represents the membrane of the cell.
- Segment and subtract the nuclei from the combined cytoplasm and
nuclei mask to give a cytoplasm mask.
- The end result is three masks; one each representing membrane,
nuclei and cytoplasm.

I can create these masks for each slice of a confocal set and get
intensity etc information out from MetaMorph. I have tried exporting the
mask stacks out to Imaris to create 3D masks but it doesn't work very
well, especially for the membrane mask, as the slices don't necessarily
overlap so there are gaps in the mask. My 3D model of the membrane masks
looks more like a badly piled up lot of rubber bands. The 3D masks for
the whole cell or nucleus work fine.

So i guess the main question is: is it possible in Imaris to do
subtractive image mathematics?



Thanks


Cam



Cameron J. Nowell
Microscopy Manager
Centre for Advanced Microscopy
Ludwig Institute for Cancer Research
PO Box 2008
Royal Melbourne Hospital
Victoria, 3050
AUSTRALIA
Office: [phone]
Mobile: [phone]
Fax: [phone]
Facility Website

[Eric Scarfone]

"is it possible in Imaris to do
subtractive image mathematics?"

not with the standard modules I din't think.

But there is a ImarisXT modulethat lest you access, from Imaris, applications developped with other software. That gives also access to a whole library of customer developped appications where you could find what you are looking for!

Good luck

Eric


Eric Scarfone, PhD, CNRS,
Center for Hearing and communication Research
Department of Clinical Neuroscience
Karolinska Institutet

Postal Address:
CFH, M1:02
Karolinska Hospital,
SE-171 76 Stockholm, Sweden

Work: [phone],
Cell: [phone]
Fax: [phone]

email: [hidden email]
http://www.ki.se/cfh/


----- Original Message -----
From: Cameron Nowell <[hidden email]>
Date: Wednesday, July 15, 2009 8:15 am
Subject: 3D Eroded Object Masks
To: [hidden email]

> I am trying to segment out membrane, cytoplasm and nuclei from a
> confocal image set. This is so we can measure translocation of a
> proteinfrom the membrane to the cytoplasm/nucleus over time. I can
> do this in
> MetaMorph but would like to be able to do it in 3D in Imaris if
> possible.
>
> The sample is stained as follows

> - Nuclei - DAPI
> - Whole Cell - CellMask (Invitrogen)
> - Protein of Interest (Alexa Antibody)
>
> Since there is not a specific stain from membrane or cytoplasm i have
> been doing the following
> - Segment out whole cells and create a binary mask
> - Erode that mask by 4 or so pixels, this represents the cytoplasm
> and nuclei of the cell
> - Subtract the eroded mask from the whole cell mask. This leave a
> ring that represents the membrane of the cell.
> - Segment and subtract the nuclei from the combined cytoplasm and
> nuclei mask to give a cytoplasm mask.
> - The end result is three masks; one each representing membrane,
> nuclei and cytoplasm.
>
> I can create these masks for each slice of a confocal set and get
> intensity etc information out from MetaMorph. I have tried
> exporting the

> mask stacks out to Imaris to create 3D masks but it doesn't work very

> well, especially for the membrane mask, as the slices don't
> necessarilyoverlap so there are gaps in the mask. My 3D model of
> the membrane masks
> looks more like a badly piled up lot of rubber bands. The 3D masks for
> the whole cell or nucleus work fine.
>
> So i guess the main question is: is it possible in Imaris to do
> subtractive image mathematics?
>
>
>
> Thanks
>
>
> Cam
>
>
>
> Cameron J. Nowell
> Microscopy Manager
> Centre for Advanced Microscopy
> Ludwig Institute for Cancer Research
> PO Box 2008
> Royal Melbourne Hospital
> Victoria, 3050
> AUSTRALIA
> Office: [phone]
> Mobile: [phone]
> Fax: [phone]
> Facility Website
>

[Daniel James White]

Hi Cameron,


On Jul 16, 2009, at 7:03 AM, CONFOCALMICROSCOPY automatic digest  
system wrote:

> Date:    Wed, 15 Jul 2009 15:52:27 +1000
> From:    Cameron Nowell <[hidden email]>
> Subject: 3D Eroded Object Masks
>
> I am trying to segment out membrane, cytoplasm and nuclei from a
> confocal image set. This is so we can measure translocation of a  
> protein
> from the membrane to the cytoplasm/nucleus over time. I can do this in
> MetaMorph but would like to be able to do it in 3D in Imaris if
> possible.

why not use ImageJ (or rather even Fiji - is just image|J batteries  
included)?
... its free....

>
> The sample is stained as follows
> - Nuclei - DAPI
> - Whole Cell - CellMask (Invitrogen)
> - Protein of Interest (Alexa Antibody)
>
> Since there is not a specific stain from membrane or cytoplasm i have
> been doing the following
> - Segment out whole cells and create a binary mask
> - Erode that mask by 4 or so pixels, this represents the cytoplasm
> and nuclei of the cell
> - Subtract the eroded mask from the whole cell mask. This leave a
> ring that represents the membrane of the cell.
> - Segment and subtract the nuclei from the combined cytoplasm and
> nuclei mask to give a cytoplasm mask.
> - The end result is three masks; one each representing membrane,
> nuclei and cytoplasm.

sounds logical!

>
> I can create these masks for each slice of a confocal set and get
> intensity etc information out from MetaMorph. I have tried exporting  
> the
> mask stacks out to Imaris to create 3D masks but it doesn't work very
> well, especially for the membrane mask, as the slices don't  
> necessarily
> overlap so there are gaps in the mask. My 3D model of the membrane  
> masks
> looks more like a badly piled up lot of rubber bands. The 3D masks for
> the whole cell or nucleus work fine.=20

i would expect that to me the case if your z resolution / sampling is  
not high enough.
This is a 3d case so you could probably sacrifice some xy resolution
by opening the pinhole to 2 airy units,
and making more z slices, so that the membrane masks overlap better.

>
> So i guess the main question is: is it possible in Imaris to do
> subtractive image mathematics?

who knows, maybe you shouldf ask them.

In Fiji - imageJ you can do things like that with a bit of Jython  
scripting.

for free, and once you learn how to do it, you could share that info  
in a tutorial on the Fiji Wiki.
Then other people profit from your efforts.

if you need help, just ask

Dan



Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

[phone] (German Mobile)
+49  (0)351 210 2627 (Work phone at MPI-CBG)
+49  (0)351 210 1078 (Fax MPI-CBG LMF)

http://www.bioimagexd.net  BioImageXD
http://pacific.mpi-cbg.de                Fiji is just ImageJ - Batteries Included
http://www.chalkie.org.uk
[hidden email]
( [hidden email] )