search

ome / bioformats

Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.
https://www.openmicroscopy.org/bio-formats
GNU General Public License v2.0
378 stars 241 forks source link

TIFF to TIFF conversion is corrupted #2798

Closed felixveysseyre closed 6 years ago

felixveysseyre commented 7 years ago

Hello,

I am using bfconvert executable to extract images from a TIFF file: bfconvert -bigtiff -series 0 "input.tiff" ".../output.%z.%t.%c.tiff"

The process run correctly but at the end the TIFF image output.0.0.0.tiff seems corrupted: capture d ecran 2017-03-22 a 15 54 31

Here is the data for which I got the issue.

I am using bfconvert 5.4.0.

Thanks for your time and your tools !

dgault commented 7 years ago

Hi Felix,

I have been testing this morning with the sample file provided and the command line tools from Bio-Formats 5.4.0. So far I have unable to recreate the same 'noise' as you are seeing it.

A couple of basic questions I would have to start:

felixveysseyre commented 7 years ago

Hello David,

I can confirm I am using latest bftools executables:

Version: 5.4.0 Build date: 20 March 2017

But the same error was also occurring with 5.3.3.

I have tested this behavior on both Ubuntu (14.04) and MacOS (10.11).

I am not able to display directly the output.0.0.0.tiff file. I tried :

Do you advise any viewer for MacOS or Ubuntu ?

The output.0.0.0.tiff file is later tiled into multiple JPEG files thanks to a C++ executable built on top of ITK and SCIFIO. It corresponds to the image I uploaded for this issue.

Since I was not able to open the output.0.0.0.tiff, file I supposed it came from bfconfert.

Thanks for your time !

felixveysseyre commented 7 years ago

@dgault Do you any news ?

dgault commented 7 years ago

Hi Felix,

Firstly apologies for the delayed response, the output.0.0.0.tiff would indeed be the file generated from the bfconvert command you were using. A simple way to view this output would be to use the showinf command which is available along with bfconvert as part of the Bio-Formats command line tools .

showinf output.0.0.0.tiff will read and print the metadata from the output file and an image viewer will open. Due to the filesize this may be quite memory intensive.

Another option would FIJI (https://fiji.sc/) which comes with Bio-Formats included. Once installed you can read files using Plugins -> Bio-Formats -> Bio-Formats Importer

sbesson commented 6 years ago

This issue has been addressed and has no further activity. It is therefore being closed. Thank you for your contributions, they are much appreciated.