Hi Mike,
Good question.... it gives me chance to vent some of my strong
opinions on this subject!
1) We have a policy in place: "Data older than one month will be
deleted from microscope system computers"
This is on a very clear large notice at the microscope that users can
not ignore.
It is not our responsibility to look after users data.
We have enough to do to keep the scopes running.
We have a computer department to deal with data security and backups.
2) We have local disk data storage on a separate physical disk in the
microscope computer.
We don't back that up. but we do back up the C: drive - operating
systems and software every 6 months,
in case of a system crash that leaves the scope non usable.
We have and to use that backup to revive a system once or twice.
We use Acronis and Norton Ghost for that.
3) We have a institute file server system, where every user has plenty
of space to put their files.
This is big infrastructure, but very much work the effort.
It is all backed up to tape by a robot every night, and data is pretty
secure.
I recommend that people save data DIRECTLY to their fileserver space,
instead of the local hard disk. Then they have the data where they
want it already
and its backed up automatically, and it doesnt fill up the local disks,
and they dont waste potential microscopy imaging time moving files to
the server.
We have gigabit ethernet in house, and i have not seen a confocal
laser point scanning system
yet that can push data to the file server faster then our network and
fileserver can handle.
This might not be true for fast widefield systems with DDC cameras.
4) In order to get around the problem of the network and fileserver
not being fast enough,
we are investigating having a cache server with many fast solid state
disks and a 10 Gigabit
connection to the microscopes that need it. data on the cache server
is then moved to the fileserver,
as fast as it can keep up, then is removed from the cache server. This
is just an idea so far.
5) We are required by law to archive all data that is generated.
We are looking at OME / OMERO and in house solutions for that.
Right now it is up to users to take care of that,
but we could really use a systems that works. My hopes lie in OMERO.
6) All our microscope systems are running sophos antivirus.
We have noticed that some systems are slowed down by it sometimes.
But we must run antivirus (on read only) because all our scopes
computers
are able to see the internet, and people do infect the systems with
viruses from USB hard disks.
FACT.
7) We strongly encourage microscope software providers to use a secure
platform
and write their software such that it plays nice with antivirus
software.
This is a necessity, not an option that would be a nice thing... if
they could be bothered.
The fact that we have to run windows on most systems is really a
problem for our IT support.
They would much rather run OSX machines and linux machines only, for
obvious reasons.
As a community we should DEMAND that software for driving microscope
systems
is not locked into an insecure windows only environment, but works on
a secure OS like SELinux or OSX.
Micromanager exists, for driving microscopes, in a free open source
and secure environment,
and as a community we should put resources towards it (free doesnt
mean it costs nothing to develop)
8) On a similar theme, we as a community should demand that the
microscope software providers implement open standards
for data formats and meta data availability.
The OME TIFF standard has been around for a while, and some software
supports it,
but all serious software should.
The fact that we have a multitude of different formats, different
between each manufacturer,
or even different within one company, is truly ridiculous.
In a recent format war on the next generation of DVDs, a SINGLE
standard won.
The open source community of working very hard to support all these
different formats
in ImageJ and other free software. This is the LOCI bio-formats project.
We must support this project as a community with resources, feedback
and resolve.
The open standards work of the OME project, in defining open standard
data structures for images and image metadata
is also very very much in need of all our support as a community.
Parting shots:
The reason we suffer every day from having to run Microsoft windows on
microscope systems,
and battle file format compatibility problems and meta data loss is
because we as a community
have not been smart enough in the past to tell the manufactures what
we really want.
Vendor lock-in is a dirty marketing strategy, but does work.
We get stuck with more of the same over and over again.
We should be aware of it, and fight against it.
It is against our interests, as a community.
We want and need open standards, microscope system flexibility and
customisation and cost effectiveness.
They think we want windows, because they think that's what people
want, because they already know windows.
some manufacturers have already figured out that this is plain WRONG.
For example Applied Precision uses a Linux operating system for the
Deltavision systems, and users LIKE that.
System administrators like it even better!
There have always ben mac users in science, and these days more and
more people have macs.
More and more people also have linux as their day to day operating
system.
There is no reason for microscopy systems software to run on windows
in favour of Linux or Mac OSX.
It is only the extra cost for the companies of porting or re writing
the software that prevents us getting linux and Max OSX versions.
Most software developers would rather use Linux as a development
platform,
but often are forced into windows because their bosses think that the
customers want windows software.
If software is written properly , it runs on all platforms ....
see ImageJ or BioImageXD.
Sure hardware drivers are platform specific....
but we should demand the platform we want,
and demand that the data is savable in an open standard (OME-TIFF)
It is up to us to demand these things.
If we remain silent, then vendor lock in continues,
and no one will bother adopting or helping to implement open standards.
We have to FORCE the companies to do that.
Some are very open to that already... usually the smaller companies.
We should encourage them as much as possible.
just my 2 cents
Dan
Begin forwarded message:
> Date: Thu, 9 Jul 2009 16:51:54 -0400
> From: Mike Tighe <[log in to unmask]>
> Subject: I.T. questions
>
> Would anyone be willing to share some of your Ideas on managing data =
> generated on single and multi photon instruments? Do you allow users
> to =
> move data directly to institute server? Has anyone tried to estimate
> the =
> amount of data per person or per hour of usage that is generated.
> How =
> often do you remove data from instrument computer? Any advice would
> be =
> very useful!
>
> Thanks!!
> Mike
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
+49 (0)15114966933 (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
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