FLEX Opera files

[Marcia Boulina]

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Dear Listserv,
I am looking for the least painful way to handle FLEX files without Columbus. Freshly updated FIJI won't open my files(but i think files are not corrupted, since someone analyzed them with Columbus before). I have forwarded a file to Kevin  and hope to get an answer, but who knows))) Gimp opens the file but image doesnt look right(looks like weird barcode, not cells)+meta is lost. I have requested a trial from Volocity, but Perkin Elmer document on how to convert FLEX to tif in Volocity  is not available on their website. Perkin support was not helpful . I have found couple Py scrips, but they also failed. We do not have OMERO yet. I am happy to hear suggestions and comments))  Thanks in advance!!!

[Emmanuel Gustin]

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Hi Marcia,

If I remember correctly, FLEX files came in two flavours. The easiest one was an uncompressed TIFF format with some extra metadata in the header.

But the alternative (and if I remember well, default) setting on the old Opera QEHS was to generate lossless compressed FLEX files using LuraWave compression. If you have compressed files, Fiji/BioFormats supports the reading, but you need to have your own copy of the LuraWave codec installed for it to work, see
https://docs.openmicroscopy.org/bio-formats/6.1.0/formats/evotecperkinelmer-opera-flex.html

I'm not sure who can supply you with that. (I don't seem to have retained a copy.) But PerkinElmer is probably still including it with Columbus, so that team should be able to help.

Emmanuel



-----Original Message-----
From: Confocal Microscopy List <[hidden email]> On Behalf Of Marcia Boulina
Sent: Thursday, 22 October 2020 19:25
To: [hidden email]
Subject: [EXTERNAL] FLEX Opera files

WARNING: This email originated from outside the company. Do not click on links unless you recognize the sender and have confidence the content is safe. If you have concerns about this email, send it as an attachment to ‘[hidden email]’.

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Dear Listserv,
I am looking for the least painful way to handle FLEX files without Columbus. Freshly updated FIJI won't open my files(but i think files are not corrupted, since someone analyzed them with Columbus before). I have forwarded a file to Kevin  and hope to get an answer, but who knows))) Gimp opens the file but image doesnt look right(looks like weird barcode, not cells)+meta is lost. I have requested a trial from Volocity, but Perkin Elmer document on how to convert FLEX to tif in Volocity  is not available on their website. Perkin support was not helpful . I have found couple Py scrips, but they also failed. We do not have OMERO yet. I am happy to hear suggestions and comments))  Thanks in advance!!!

[Maria Y. Boulina]

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Thank you, Emmanuel!
 LuraWave did somewhat help! I could see the metadata in fiji! but not to
open anything))
Now we are trying to convert files inside the Opera using help from
Perkin., Stay tuned.
M

пн, 26 окт. 2020 г. в 06:56, Gustin, Emmanuel [JRDBE] <[hidden email]>:

> *****
> 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.
> *****
>
> Hi Marcia,
>
> If I remember correctly, FLEX files came in two flavours. The easiest one
> was an uncompressed TIFF format with some extra metadata in the header.
>
> But the alternative (and if I remember well, default) setting on the old
> Opera QEHS was to generate lossless compressed FLEX files using LuraWave
> compression. If you have compressed files, Fiji/BioFormats supports the
> reading, but you need to have your own copy of the LuraWave codec installed
> for it to work, see
>
> https://docs.openmicroscopy.org/bio-formats/6.1.0/formats/evotecperkinelmer-opera-flex.html
>
> I'm not sure who can supply you with that. (I don't seem to have retained
> a copy.) But PerkinElmer is probably still including it with Columbus, so
> that team should be able to help.
>
> Emmanuel
>
>
>
> -----Original Message-----
> From: Confocal Microscopy List <[hidden email]> On
> Behalf Of Marcia Boulina
> Sent: Thursday, 22 October 2020 19:25
> To: [hidden email]
> Subject: [EXTERNAL] FLEX Opera files
>
> WARNING: This email originated from outside the company. Do not click on
> links unless you recognize the sender and have confidence the content is
> safe. If you have concerns about this email, send it as an attachment to ‘
> [hidden email]’.
>
> *****
> 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.
> *****
>
> Dear Listserv,
> I am looking for the least painful way to handle FLEX files without
> Columbus. Freshly updated FIJI won't open my files(but i think files are
> not corrupted, since someone analyzed them with Columbus before). I have
> forwarded a file to Kevin  and hope to get an answer, but who knows))) Gimp
> opens the file but image doesnt look right(looks like weird barcode, not
> cells)+meta is lost. I have requested a trial from Volocity, but Perkin
> Elmer document on how to convert FLEX to tif in Volocity  is not available
> on their website. Perkin support was not helpful . I have found couple Py
> scrips, but they also failed. We do not have OMERO yet. I am happy to hear
> suggestions and comments))  Thanks in advance!!!
>