[ome-users] Problem importing multi-page tif

[posts at roeser-reichartshausen.de]

Good morning Christoph,

thank you for pointing this out. So I have to find out if I can force  
imagemagick to use the correct bit order. In the metadata, I have  
looked at with EXIFtool, I only see that the scanner image has the tag  
ExifByteOrder set to big-endian, whereas the imagemagick file has it  
set to little-endian. But I think this is not what you mean.

Can I see the bit order within the bytes somewhere easily?

Hermann-Josef

Zitat von Christoph Gohlke <cgohlke at uci.edu>:

> The Test.tif image has the logical order of bits within the bytes  
> reversed (FillOrder=2). The TIFF specification recommends against  
> using this. See  
> <http://www.awaresystems.be/imaging/tiff/tifftags/fillorder.html>.
>
> Christoph
>
>
> On 9/25/2015 9:58 AM, posts at roeser-reichartshausen.de wrote:
>> Good evening Curtis,
>>
>> the problem does not seem to be the bit-depth change, since an image
>> from my scanner with exactly this image structure as teh imagemagick one
>> is imported with bio-formats correctly. My goal was to mimick the image
>> from the scanner with imagemagick but got stuck with this problem.
>>
>> I will upload the image to the bio-format team with comments.
>>
>> Best wishes
>>
>> Hermann-Josef
>>
>>
>> Zitat von Curtis Rueden <ctrueden at wisc.edu>:
>>
>>> Hi Hermann-Josef,
>>>
>>> Thanks for the sample. I added it to our collection for SCIFIO, where we
>>> already have an issue filed for this problem:
>>>
>>>  https://github.com/scifio/scifio/issues/159
>>>
>>> In your case, it's a different bit depths rather than different
>>> dimensions,
>>> but the problem is the effectively the same.
>>>
>>> Sorry to say I don't have a timeline for fixing this, but it's on our
>>> radar.
>>>
>>> On the Bio-Formats side, I'm not sure whether there is an issue tracking
>>> this limitation yet.
>>>
>>> Regards,
>>> Curtis
>>>
>>> On Thu, Sep 24, 2015 at 10:08 AM, <posts at roeser-reichartshausen.de>
>>> wrote:
>>>
>>>> Hi Curtis,
>>>>
>>>> a sample image is on my server:
>>>> http://www.roeser-reichartshausen.de/Scans/Test.tif (250 MB)
>>>>
>>>> Thank you for looking into this.
>>>>
>>>> Hermann-Josef
>>>>
>>>>
>>>> Zitat von Curtis Rueden <ctrueden at wisc.edu>:
>>>>
>>>>
>>>> Hi Hermann-Josef,
>>>>>
>>>>> Can you share a sample image?
>>>>>
>>>>> Regards,
>>>>> Curtis
>>>>>
>>>>> On Thu, Sep 24, 2015 at 3:42 AM, <posts at roeser-reichartshausen.de>
>>>>> wrote:
>>>>>
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> my multi-page tif image, created with imagemagick, contains a
>>>>>> 3x16bit RGB
>>>>>> image on page 1 and a 1x16bit B&W image on page 2. This image is not
>>>>>> correctly imported with bio-formats 5.1.4 into imageJ. However, it is
>>>>>> correctly opened in GIMP2 and IrfanView. So I suspect, there is a
>>>>>> problem
>>>>>> with bio-formats input. However, other images with the same
>>>>>> structure but
>>>>>> from a source different to imagemagick are imported correctly.
>>>>>>
>>>>>> Does anybody know this problem and a possible solution?
>>>>>>
>>>>>> Hermann-Josef
>>>>>>
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