slide scanning services - do you have a file naming convention?

[Cromey, Douglas W - (dcromey)-2]

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Hello all,

We are getting ready to fire up a slide scanning service (lab staff doing the scanning for users) and I am wondering if people have file naming conventions for the data that you collect. Our user's requests will be submitted through iLab, so the requests will get a unique project number there. Do you include the date it was scanned (I'm thinking the ISO date standard of YYYY-MM-DD)? Do you use folder names in a particular way?

Thanks for the feedback (any other tips, tricks or pitfalls are appreciated as well), I'm just trying to sort this out before the avalanche of data happens...

Doug

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Douglas W. Cromey, M.S. - Associate Scientific Investigator
Dept. of Cellular & Molecular Medicine, University of Arizona
Life Sciences North, Room 463
1333 N. Martin Ave, Tucson, AZ  85721 USA

office:  LSN 463        email: [hidden email]<mailto:[hidden email]>
voice:  520-626-2824       fax:  [phone]

UA Microscopy Alliance - http://microscopy.arizona.edu/
A collaborative effort to bring information about shared microscopy
facilities to the University of Arizona and the community.

[Craig Brideau]

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Your best bet is to invest in some sort of database software to manage the
incoming torrent of information. A good system will provide a user client
that allows you to create a project, then link individual experimental
entries to a given project. The experimental entries would include your
slide scanning data and link back to the project entry, which would include
ongoing and overall information on the project. You can then use a client
to search for experiments and link back to the project; this lets you
quickly switch from a "ground level" to "birds-eye view" of your project so
you can keep tabs on the overall progress of your research.

Craig

On Thu, Jan 28, 2021 at 7:28 AM Cromey, Douglas W - (dcromey) <
[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Hello all,
>
> We are getting ready to fire up a slide scanning service (lab staff doing
> the scanning for users) and I am wondering if people have file naming
> conventions for the data that you collect. Our user's requests will be
> submitted through iLab, so the requests will get a unique project number
> there. Do you include the date it was scanned (I'm thinking the ISO date
> standard of YYYY-MM-DD)? Do you use folder names in a particular way?
>
> Thanks for the feedback (any other tips, tricks or pitfalls are
> appreciated as well), I'm just trying to sort this out before the avalanche
> of data happens...
>
> Doug
>
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> Douglas W. Cromey, M.S. - Associate Scientific Investigator
> Dept. of Cellular & Molecular Medicine, University of Arizona
> Life Sciences North, Room 463
> 1333 N. Martin Ave, Tucson, AZ  85721 USA
>
> office:  LSN 463        email: [hidden email]<mailto:
> [hidden email]>
> voice:  520-626-2824       fax:  [phone]
>
> UA Microscopy Alliance - http://microscopy.arizona.edu/
> A collaborative effort to bring information about shared microscopy
> facilities to the University of Arizona and the community.
>

[Praju Vikas Anekal]

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Dear Doug,

the naming convention will probably be dictated by the system you have.
e.g. File name lengths might be restricted in some instances or space/special characters may not be allowed.

Any downstream analysis you/the users might require can also have an impact.
e.g. Opening up files in ImageJ/Fiji, if special characters are present, might require some macro coding to extract the core names etc...

Nomenclature that we recommend for Slide scanner files is
<user initials (2-3char max)> _<Date(yymmdd)> _ <magnification or objective used (10x or 20x)> _ <tissue/case type> _ <running number>_
e.g. PV_210129_10x_Brain5043_01_

if space is available still, it is also useful to include the antibody/labels used and wavelength but usually this is quite long and some for a shorthand is useful here

This  has been our suggestions but some users have their own lab established naming conventions which they use

Cheers :)

Yours sincerely,

Praju Vikas Anekal. Ph.D.
Biomed Imaging Microscopist/BioImage Analyst, Biomedical Imaging Research Unit.
Faculty of Medical and Health Sciences, The University of Auckland.
E-Mail : [hidden email]<mailto:[hidden email]> , Ext : 87831

From: Confocal Microscopy List <[hidden email]> On Behalf Of Cromey, Douglas W - (dcromey)
Sent: Friday, 29 January 2021 3:27 AM
To: [hidden email]
Subject: slide scanning services - do you have a file naming convention?

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy<http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>
Post images on http://www.imgur.com<http://www.imgur.com> and include the link in your posting.
*****

Hello all,

We are getting ready to fire up a slide scanning service (lab staff doing the scanning for users) and I am wondering if people have file naming conventions for the data that you collect. Our user's requests will be submitted through iLab, so the requests will get a unique project number there. Do you include the date it was scanned (I'm thinking the ISO date standard of YYYY-MM-DD)? Do you use folder names in a particular way?

Thanks for the feedback (any other tips, tricks or pitfalls are appreciated as well), I'm just trying to sort this out before the avalanche of data happens...

Doug

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Douglas W. Cromey, M.S. - Associate Scientific Investigator
Dept. of Cellular & Molecular Medicine, University of Arizona
Life Sciences North, Room 463
1333 N. Martin Ave, Tucson, AZ 85721 USA

office: LSN 463 email: [hidden email]<mailto:[hidden email]<mailto:[hidden email]%3cmailto:[hidden email]>>
voice: 520-626-2824 fax: [phone]

UA Microscopy Alliance - http://microscopy.arizona.edu/<http://microscopy.arizona.edu>
A collaborative effort to bring information about shared microscopy
facilities to the University of Arizona and the community.

[Konstantín Levitskiy]

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*****

It could also be possible that users have a barcode marking their preparations, like in the hospital service. Some slide scanners, as I've heard, have the possibility to recognize them and save as the preparation is marked.
Best and safe regards,
Konstantin
________________________________
De: Confocal Microscopy List <[hidden email]> en nombre de Praju Vikas Anekal <[hidden email]>
Enviado: viernes, 29 de enero de 2021 0:13
Para: [hidden email] <[hidden email]>
Asunto: Re: slide scanning services - do you have a file naming convention?

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Dear Doug,

the naming convention will probably be dictated by the system you have.
e.g. File name lengths might be restricted in some instances or space/special characters may not be allowed.

Any downstream analysis you/the users might require can also have an impact.
e.g. Opening up files in ImageJ/Fiji, if special characters are present, might require some macro coding to extract the core names etc...

Nomenclature that we recommend for Slide scanner files is
<user initials (2-3char max)> _<Date(yymmdd)> _ <magnification or objective used (10x or 20x)> _ <tissue/case type> _ <running number>_
e.g. PV_210129_10x_Brain5043_01_

if space is available still, it is also useful to include the antibody/labels used and wavelength but usually this is quite long and some for a shorthand is useful here

This  has been our suggestions but some users have their own lab established naming conventions which they use

Cheers :)

Yours sincerely,

Praju Vikas Anekal. Ph.D.
Biomed Imaging Microscopist/BioImage Analyst, Biomedical Imaging Research Unit.
Faculty of Medical and Health Sciences, The University of Auckland.
E-Mail : [hidden email]<mailto:[hidden email]> , Ext : 87831

From: Confocal Microscopy List <[hidden email]> On Behalf Of Cromey, Douglas W - (dcromey)
Sent: Friday, 29 January 2021 3:27 AM
To: [hidden email]
Subject: slide scanning services - do you have a file naming convention?

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy<http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy>
Post images on http://www.imgur.com<http://www.imgur.com> and include the link in your posting.
*****

Hello all,

We are getting ready to fire up a slide scanning service (lab staff doing the scanning for users) and I am wondering if people have file naming conventions for the data that you collect. Our user's requests will be submitted through iLab, so the requests will get a unique project number there. Do you include the date it was scanned (I'm thinking the ISO date standard of YYYY-MM-DD)? Do you use folder names in a particular way?

Thanks for the feedback (any other tips, tricks or pitfalls are appreciated as well), I'm just trying to sort this out before the avalanche of data happens...

Doug

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Douglas W. Cromey, M.S. - Associate Scientific Investigator
Dept. of Cellular & Molecular Medicine, University of Arizona
Life Sciences North, Room 463
1333 N. Martin Ave, Tucson, AZ 85721 USA

office: LSN 463 email: [hidden email]<mailto:[hidden email]<mailto:[hidden email]%3cmailto:[hidden email]>>
voice: 520-626-2824 fax: [phone]

UA Microscopy Alliance - http://microscopy.arizona.edu/<http://microscopy.arizona.edu>
A collaborative effort to bring information about shared microscopy
facilities to the University of Arizona and the community.

[Denise Ramirez]

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Hi Doug,

We have 2 slide scanners in our facility and offer training to individual users as well as slide scanning at a service (for an extra fee). Both of our systems have a default file naming strategy that is essentially a time/day stamp although different in formatting between the two systems. In the case where we are scanning as a service, we generally don't offer to specify the file names for the client and just use the default time day stamps. It's straightforward to import a pre-populated list for 1 of my systems but a big pain in the other. I figure if they need to change the filename they can do that on their own later on, especially in cases of specific character/length restrictions for coding purposes. We store the images temporarily on our cluster and send the user a link to download the files. I just have a folder system set up for each lab with individual users within that. We don't have the volume that it's difficult to keep track of yet, though in the pandemic our drop off slide scanning services have definitely increased. Hope it helps!