[ome-users] intensity scaling problem when saving a .dv file

[Kai Schleicher]

Hi,

I am having a curious problem when saving a 16-bit *.dv file (ID 17471 
on your sever). Please find below the code to see what exactly I did.

In brief I open the raw data with the BF-importer, split the two 
channels, close channel 0 and export channel 1 using the BF-exporter.

When I then open the just saved image using the BF-importer, it appears 
to be on a different intensity-scale (see attached screenshot).

My guess is that there's something wrong with the raw data since this 
problem appears when using the BF-exporter as well as when using FIJIs 
own "save as -> tiff". The problem also appears when exporting as 
ome-tiff rather then tif.

Thanks for your help and cheers,
Kai

-------
run("Bio-Formats Importer", "open=/home/kai/DATA/IMCF/raw/raw_data.dv 
autoscale color_mode=Default rois_import=[ROI manager] split_channels 
view=Hyperstack stack_order=XYCZT");
selectWindow("raw_data.dv - C=0");
close();
wait(1000); // imagej-voodoo
selectWindow("raw_data.dv - C=1");
run("Bio-Formats Exporter", 
"save=/home/kai/DATA/IMCF/raw/resaved_data.tif compression=Uncompressed");
run("Bio-Formats Importer", 
"open=/home/kai/DATA/IMCF/raw/resaved_data.tif autoscale 
color_mode=Default rois_import=[ROI manager] view=Hyperstack 
stack_order=XYCZT");
selectWindow("raw_data.dv - C=1");
run("Histogram");
selectWindow("resaved_data.tif");
run("Histogram");
selectWindow("raw_data.dv - C=1");
resetMinAndMax();



-- 

>>Please note my NEW PHONE NUMBERS: +41 61 207 57 31 (direct) +41 61 207 22 50 (central)<<
Kai Schleicher, PhD | Research Associate in Advanced Light Microscopy | Biozentrum, University of Basel | Klingelbergstrasse 50/70 | CH-4056 Basel |
Phone: +41 61 207 57 31 (direct) +41 61 207 22 50 (central) | kai.schleicher at unibas.ch | www.biozentrum.unibas.ch | www.microscopynetwork.unibas.ch

-------------- next part --------------
A non-text attachment was scrubbed...
Name: screenshot.png
Type: image/png
Size: 213101 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20161213/7beacbee/attachment.png>