[ome-users] Error while converting Leica .scn files to tiff format

[David Gault (Staff)]

Hi Hitesha,

When converting from Leica SCN to TIFF you are probably going to see a large jump in file size. From your output you seem to being using LZW compression which should help reduce the output size somewhat but it will still be larger than the original.
I suspect the errors when attempting to read the files may be due to memory constraints but we would need to test the file to confirm. If you are able to upload the original scene file to https://www.openmicroscopy.org/qa2/qa/upload/ then we can check and confirm if the generated tiff is indeed valid or if there has been an issue during conversion.

With Thanks,
David Gault

On 11 Dec 2018, at 20:50, MS2016007 Hitesha Mukherjee <hitesha.mukherjee at iiitb.org<mailto:hitesha.mukherjee at iiitb.org>> wrote:

 Hello Team,

I have been trying Bio-Formats to convert my image which is in scn format (Leica scn) using the command line bftools.zip.  I have received Converted TIFF files which are huge in size (6GB and 4 GB respectively) as compared to the original .scn file (300 MB ) . The images do not open at all in any specialized software. Details of the error  are as follows:

bftools latest version : A bundle of scripts for using Bio-Formats on the command line with bioformats_package.jar already included.  Windows Operating system with 4 GB RAM. I have included in the attachment all the information.

I am unable to open the converted image in any other software as well.

Details like width, height, number of channels, Z slices, and timepoints are attached in the screenshots.

Please look into it and advise accordingly.

Warm Regards,
Hitesha


<windowsversion.PNG><detailsof image2.PNG><detailsofimage1.PNG><detailsofimage3.PNG><errorinopeningfile_4GBsize.PNG><bftoolsdetails (2).PNG><bftoolsdetails.PNG><erroropeningTIFFfile.PNG>_______________________________________________
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