LeeKamentsky
commented
9 years ago I read her post the other day - I think she's has correctly pointed out why there's a discrepancy. You can follow the directions in that issue if you want to get the image reader that you'd get in Java.
On Sun, May 10, 2015 at 7:52 AM, sebi06 notifications@github.com wrote:
Hi guys,
Melissa Linkert pointed me towards you since she thinke this issue might be relateted to:
ttps://github.com/CellProfiler/python-bioformats/issues/23
Is this the case?
Sebi
Here is my original mail for the OME people:
Hi guys,
i encounter a strange behavior and I am not sure, if this is a bug or I do something wrong.
This is the z-Stack: https://dl.dropboxusercontent.com/u/623476/Beads_63X_NA1.35_xy%3D0.042_z%3D0.1.czi
When I open this via Fiji (up-to-date 20150508) I get a z-Stack with 100 focal planes - OK --> see screenshot
[image: screenshot1] https://cloud.githubusercontent.com/assets/3833249/7554122/9089c450-f71b-11e4-9630-569d252fe6ee.png
When I load this CZI vai Python Bioformats (bioformats_package 5.1.1 + python_bioformats 1.0.4) , it also works fine --> see screenshot
[image: screenshot2] https://cloud.githubusercontent.com/assets/3833249/7554123/99855c0e-f71b-11e4-9c58-653f943f9e48.png
Now I go back to Fiji and use the BioFormats exporter to write an OME-TIFF from the open CZI and save it to disk.
File can be found here: https://dl.dropboxusercontent.com/u/623476/63X_NA1.35_xy%3D0.042_z%3D0.1.ome.tiff
When I open the OME-TIFF in Fiji I get a z-stack with 100 planes and the correct z.spacing (as expected). But when I open the OME-TIFF via python-bioformats The dimensions get mixed up --> see screenshot below.
So I am wondering why the python stuff seems to work for the CZI, but not for the exported OME-TIFF while it always seems to be OK for Fiji itself no matter if I open the CZI or the exported OME-TIFF.
And why is the z-spacing wrong? I think because the python assumes it is a NOT a z-stack.
Sebi
[image: screenshot3] https://cloud.githubusercontent.com/assets/3833249/7554124/a2838718-f71b-11e4-93b6-e65a71e5711b.png
— Reply to this email directly or view it on GitHub https://github.com/CellProfiler/python-bioformats/issues/26.
sebi06
Hi guys,
Melissa Linkert pointed me towards you since she thinke this issue might be relateted to:
ttps://github.com/CellProfiler/python-bioformats/issues/23
Is this the case?
Sebi
Here is my original mail for the OME people:
Hi guys,
i encounter a strange behavior and I am not sure, if this is a bug or I do something wrong.
This is the z-Stack: https://dl.dropboxusercontent.com/u/623476/Beads_63X_NA1.35_xy%3D0.042_z%3D0.1.czi
When I open this via Fiji (up-to-date 20150508) I get a z-Stack with 100 focal planes - OK --> see screenshot
When I load this CZI vai Python Bioformats (bioformats_package 5.1.1 + python_bioformats 1.0.4) , it also works fine --> see screenshot
Now I go back to Fiji and use the BioFormats exporter to write an OME-TIFF from the open CZI and save it to disk.
File can be found here: https://dl.dropboxusercontent.com/u/623476/63X_NA1.35_xy%3D0.042_z%3D0.1.ome.tiff
When I open the OME-TIFF in Fiji I get a z-stack with 100 planes and the correct z.spacing (as expected). But when I open the OME-TIFF via python-bioformats The dimensions get mixed up --> see screenshot below.
So I am wondering why the python stuff seems to work for the CZI, but not for the exported OME-TIFF while it always seems to be OK for Fiji itself no matter if I open the CZI or the exported OME-TIFF.
And why is the z-spacing wrong? I think because the python assumes it is a NOT a z-stack.
Sebi