[Cytometry] archiving data in a flow core?

Mcfarlin, Brian Brian.Mcfarlin at unt.edu
Sat Feb 15 11:11:34 EST 2014

Ruth and Matthew,

Ruth I assume you may be referring to the EMD Millipore-Amnis imaging
cytometers. I can tell you that their computers come with small hard
drives (I think mine is 500 gb) for the explicit purpose of forcing you to
archive often. With that said I can fill that hard drive with data in a
4-6 weeks when we have an active project. I had to work with my IT folks
to get access to a large volume networked data storage (4 TB). For now
this is sufficient for all our archiving, but I am sure if we continue at
this pace it is going to not last long. The imaging instruments are really
amazing in terms of what data they generate, but all of those images also
generate massive amounts of data. For example we have one experiment where
we are looking at rare cell populations upon collection of a million total
events, we end up with a 1 GB data file. We have found that the size of
this file can be reduced if you turn off the channels that you are not
using, but like any cytometry you just have to be careful that you do not
accidentally turn off a channel that you need (really this is just about
good planning). 

Also on my Millipore provided computer I added a USB 3.0 card and
encourage my users to have a USB 3.0 flash drive. Without that it can take
forever to transfer data files from the computer to a flash drive. With
regard to the network infrastructure, given my data transfer needs, I was
able to convince the University to rewire my entire lab for gigabyte
ethernet. This makes a HUGE different over the standard 100mb ethernet.
Just looks for infrastructure things to consider. Some of these are
probably universal to any cytometer. Thanks and let me know how else we
can help,


Brian K. McFarlin, PhD, FACSM, FTOS
Assistant Professor Exercise Physiology & Nutrition
University of North Texas
1155 Union Circle, #310769
Physical Education Bldg, Room 209
1921 Chestnut Street
Denton, TX 76203
Phone: (940) 565-3165
Fax: (940) 565-4904
Mobile: (713) 240-5806

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On 2/14/14, 2:34 PM, "Cochran, Matthew"
<Matthew_Cochran at URMC.Rochester.edu> wrote:

>- Whenever possible (depending on hard disk space) we retain the current
>month and the previous months files on the computer so they can be easily
>re-accessed.  For our Diva instruments the FCS files are deleted weekly,
>while the Exp files follow the one-two month practice.
>- Every week during "long cleans" and QA/QC procedures we clean and defrag
>the hard drives.  This isn't a trivial process but if your hard drives are
>well organized you only need to check a couple folders per instrument per
>	- I think a well organized data storage practice is absolutely critical
>and should be the first priority if its not already.  Once the practice is
>established you instate the policy that anything not stored appropriately
>is deleted immediately.
>	- Another note on the Diva instruments: we never allow any storage of
>files within the diva software itself.  Everything has to be immediately
>exported and deleted from the software.
>- Our practice is to store/archive all files as long as they're exported
>and stored on the instrument computer appropriately.  We can accomplish
>this by using a program called Syncback that automatically scans the hard
>drive and backs up data every night.  As you said, this can be an
>expensive undertaking, but its a potentially project saving service you
>can offer and the price can be rolled back into the instrument charges.
>The biggest downside aside from price is figuring out the server or back
>up drive system that will work for you.  With any luck your IT department
>runs well and can be an asset here.
>You didn't specify what imaging cytometer you were getting but the storage
>space issue is most definitely compounded once you get into imaging files.
> We routinely generate 200-300 gb of data per month on our ISX, which can
>be pretty taxing if you're using 1tb external hard drives as backup.
>Matthew Cochran
>   Technical Director
>   URMC Flow Cytometry
>   Office Phone: 585-273-4020
>   Office Rm: 3-4113
>    http://www.urmc.rochester.edu/flow-core
>    http://www.urmc.rochester.edu/flow-core/training
>On 2/14/14 2:17 PM, "Ruth Nissly" <rah38 at psu.edu> wrote:
>>Dear flow-ers, 
>>If you are in a flow cytometry core facility, I have a question: What are
>>the policies held by your core regarding data storage & archiving?
>>-How long are users allowed to leave data on the acquisition computer?
>>-How are data files older than this time-period removed from the
>>acquisition computer?
>>-Are old files stored as backups by the core? If so, for how long are the
>>backups stored? 
>>We're getting to the point where it's taking a lot of time and money to
>>archive data that very few people actually ever request, so your
>>advice/experience would be helpful in deciding how to move forward. For
>>reference, we have files collected using CXP, Diva, Spigot, and Summit --
>>and we will soon also be getting imaging flow cytometry files.
>>Thank you, 
>>Ruth Nissly 
>>research technologist
>>Microscopy & Cytometry Facility
>>The Huck Institutes of the Life Sciences
>>Pennsylvania State University
>>W-124A Millennium Science Complex
>>University Park, PA 16802
>>rah38 at psu.edu 
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