ImageJ - Re: Network drive slowness

ImageJ

Re: Network drive slowness

Posted by Unruh, Jay-2 on Nov 11, 2014; 4:31pm
URL: http://imagej.273.s1.nabble.com/Network-drive-slowness-tp5010338p5010376.html

Is it possible to export in the older .lsm format and preserve metadata? That format was essentially a customized tiff with metadata, so the performance should be similar to tiff. In addition, there are non-bioformats options for reading that data if you want to troubleshoot. We save all confocal data as .lsm rather than .czi.

Jay

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Niko Ehrenfeuchter
Sent: Monday, November 10, 2014 5:20 PM
To: [hidden email]
Subject: Re: Network drive slowness

Dear All,

maybe I should clarify a bit my previous message:

I didn't intend *at all* to criticize Bio-Formats - in fact it is an outstanding project which is saving my ass every single day, and I
*really* appreciate it a lot!

My point was just about our general experience with using imaging data directly on network shares (which is even limited to the SMB/CIFS protocol, but this is probably true for the majority of the users here) and our persistent recommendation to work on local storage only.
Actually, we've seen *much* worse behaviour in combination with network shares from commercial software (under paid maintenance!), where the vendor is even refusing to work on these problems.

So my apologies if this came out the wrong way!

Cheers
~Niko

On 10.11.2014 23:49, Jason Swedlow wrote:

> Dear All-
>
> Just to reiterate Curtis' point, OME welcomes reports of any issues
> regarding Bio-Formats. See
>
> http://www.openmicroscopy.org/site/support/bio-formats5/about/bug-repo
> rting.html
>
> or the Bio-Formats Forum at
>
> http://www.openmicroscopy.org/community/
>
> Obviously, we won't be very helpful diagnosing the vagaries of your
> network performance. We will respond to and work on issues related to
> file opening times, etc. We've put a lot of work into CZI and other
> multi-platform file formats recently-- any and all feedback welcome.
>
> Thanks!
>
> Cheers,
>
> Jason
>
> On Mon, Nov 10, 2014 at 10:29 PM, Niko Ehrenfeuchter <
> [hidden email]> wrote:
>
>> Hi all,
>>
>> On 10.11.2014 21:13, Curtis Rueden wrote:
>>
>>> Hi Rafael,
>>>
>>> should I do a bug report for it?
>>>>
>>>
>>> The CZI support is driven by Bio-Formats [1].
>>>
>>
>> from my experience with loading / saving data from network shares,
>> I'm not sure wheter this is related to the CZI format.
>>
>> Loading images using Bio-Formats directly from a network drive
>> usually takes around 10x longer than opening the same file from a
>> local disk (whereas the storage backend of the network drive is
>> potentially a lot faster than the conventional HDD's we're using on most of our computers).
>> Sometimes it can even be up to 100x slower than opening data locally.
>>
>> The same story goes the other way round, when writing OME-TIFFs to a
>> network share. We've even had situations where the OME-TIFFs seem to
>> be written correctly but upon re-opening them they were broken.
>> Problem was that this was not reliably reproducible, so I didn't have
>> anything to file a reasonable bug report.
>>
>> The baseline of this is that we keep on telling our users to *always*
>> transfer the data onto the machines they're using to process it, do
>> their work, save it locally and then eventually transfer everything
>> back to their network share to ensure maximum speed and reliability.
>>
>> I'd be more than happy to help in improving this situation!
>>
>> Best regards,
>> ~Niko
>> --
>> Niko Ehrenfeuchter | Image Analysis Specialist | Biozentrum,
>> University of Basel | Klingelbergstr. 50/70 | CH-4056 Basel
>> Phone: +41 (61) 26 72673 | [hidden email] |
>> www.biozentrum.unibas.ch | www.microscopynetwork.unibas.ch
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
>
>