[ome-users] SCN TO TIFF CONVERSION

[David Gault (Staff)]

Hi Mohanapriya,

Thank you for uploading the sample file. I have been able to test it today and using bfconvert with the latest Bio-Formats 6.0.0 I was able to open and display the resulting tiff file. Which viewer are you using to open the file? What sort of corruption are you seeing?

With Thanks,
David Gault

On 7 Mar 2019, at 15:36, Narapareddy, Mohanapriya <mohanapriya.narapareddy at emory.edu<mailto:mohanapriya.narapareddy at emory.edu>> wrote:

Hello David,
Thanks for your reply. Since .  ‘%s’ in the conversion will split the output into a separate file for each series, and i want a single file, I used the below command.


bfconvert /path/to/input output.tiff

 The problem is the generated file is corrupted and i am unable to view it in the viewer properly. I was able to view the scn file before conversion but the tiff file generated was not the same.

Please resolve this issue. I uploaded my .scn file in the given link. Please let me know if you can properly convert it in to the tiff file.

Thanks,
Mohanapriya
________________________________
From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk<mailto:ome-users-bounces at lists.openmicroscopy.org.uk>> on behalf of David Gault (Staff) <d.gault at dundee.ac.uk<mailto:d.gault at dundee.ac.uk>>
Sent: Thursday, March 7, 2019 9:43:38 AM
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Subject: Re: [ome-users] SCN TO TIFF CONVERSION

Hi Mohanapriya,

Using ‘%s’ in the conversion will split the output into a separate file for each series. Is that what you intended? When you say that the planes are separate is it the channel fields that are separate but you wish them to be interleaved? The bfconvert command currently bases the channel interleaving of the output file as the same as the that used for the input reader.

I was unable to access the file you linked, would you be able to upload it to https://www.openmicroscopy.org/qa2/qa/upload/?

With Thanks,
David Gault

On 6 Mar 2019, at 19:36, Narapareddy, Mohanapriya <mohanapriya.narapareddy at emory.edu<mailto:mohanapriya.narapareddy at emory.edu>> wrote:

Narapareddy, Mohanapriya has shared a OneDrive for Business file with you. To view it, click the link below.


<https://emory-my.sharepoint.com/personal/mnarapa_emory_edu/Documents/Attachments/C3L.01064.21.scn>
[https://r1.res.office365.com/owa/prem/images/dc-generic_20.png]<https://emory-my.sharepoint.com/personal/mnarapa_emory_edu/Documents/Attachments/C3L.01064.21.scn>

C3L.01064.21.scn<https://emory-my.sharepoint.com/personal/mnarapa_emory_edu/Documents/Attachments/C3L.01064.21.scn>



Hello,
I am facing problem with scn to tiff conversion.
Please help me with this issue.
Here i attach my scn file.

Here is the command i used. please correct me if i am wrong.
  bfconvert -bigtiff C3L.01064.21.scn sample1-%s.tif

Thanks,
Mohanapriya

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