Dan,
First, I completely agree with the open standards rant. The mandate
should even flow from the government level, not allowing funding for
devices and systems that use proprietary formats, etc.
Now, you say in #1 that archiving data is a user responsibility (with
which I agree), but then, in #5, that you are required by law to archive
all data generated. Someone from Princeton said they are required to
archive data for 7 years. I'm just curious. I can see a research
institution or granting agency mandating the archiving of data, but
would that be the responsibility of the PI to see that the data is
archived? If they have their own instruments that would be the case. As
you say we have enough to do (as underfunded facilities) providing the
facilities for the imaging. Perhaps #5 was in reference to methods for
archiving by the PI?
Dale
Daniel James White wrote:
> 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
> [log in to unmask]
> ( [log in to unmask] )
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