Posted by
MRivers on
URL: http://imagej.273.s1.nabble.com/Bug-when-reading-RGB-TIFF-files-with-ROWSPERSTRIP-1-tp5020468p5020488.html
> due to the highly flexible TIF-definition (a generally positive property) there is an enormous variety of TIF-file types and ImageJ can't open all of them (correctly). A typical variety that poses problems are compressed TIF-files.
That is true. But in the specific case of the simple images I am discussing I believe it is a true bug in ImageJ.
First, these images open correctly in every other application I have tested, which now includes several more than my previous posts.
- The Python Imaging Library (PIL) correctly displays these files with the following:
>>> from PIL import Image
>>> im = Image.open('test_rgb2_001.tif')
>>> im.Show()
- IDL read_tiff('test_rgb2_001.tif') function returns an 3-D array that displays correctly with the IDL iimage function.
- ImageMagick correctly displays the file with the Linux "display test_rgb2_001.tif" command
- Dragging the file into a Microsoft Word document displays it correctly
- Dragging the file into a Microsoft PowerPoint document displays it correctly.
- Opening the file with Microsoft Paint displays the file correctly
- Opening the file with Microsoft Photos displays the file correctly
In fact the only application I can find that does not display the file correctly is ImageJ.
Moreover, if ImageJ does not understand the TIFF file it should report a warning or error. However, it does not report any problem. It acts as if it correctly read the file, but the image displayed in ImageJ is completely wrong.
I really believe this is a bug in ImageJ.
Mark
-----Original Message-----
From: Herbie [mailto:
[hidden email]]
Sent: Monday, April 16, 2018 8:48 AM
To: Mark Rivers <
[hidden email]>;
[hidden email]
Subject: Re: Bug when reading RGB TIFF files with ROWSPERSTRIP=1
Mark,
due to the highly flexible TIF-definition (a generally positive
property) there is an enormous variety of TIF-file types and ImageJ can't open all of them (correctly). A typical variety that poses problems are compressed TIF-files.
BioFormats copes with more TIF-types and most of them it opens without further processing.
I understand that the steps I've proposed aren't suited for opening files on a regular basis. Therefore, I suggest to contact the BioFormats-team and provide typical images that pose problems. In general, they will have a look at them and if possible provide a dedicated solution. This means that you may then be able to open such images via BioFormats directly, i.e. without any further steps or settings.
Regards
Herbie
:::::::::::::::::::::::::::::::::::::::::
Am 16.04.18 um 15:36 schrieb Mark Rivers:
> Hi Herbie,
>
>> Yes Mark,
>> it is an ImageJ-plugin:
>> <
https://www.openmicroscopy.org/bio-formats/downloads/>
>> Please try with BioFormats and please report about your result.
>
>> Regards
>> Herbie
>
>
> Yes, I can read these images with Bioformats as you described. However, that is rather inconvenient. These are perfectly valid TIFF files which can be opened with no problems in other applications (IDL, ImageMagick, Photos, Paint, etc.) so I believe they should open correctly with the built-in ImageJ TIFF reader. The built-in TIFF reader opens them but completely incorrectly.
>
> Thanks,
> Mark
>
>
>
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