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help > LSM file reading
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Jul 23, 2010 12:07 AM | Hanchuan Peng
LSM file reading
Dan,
V3D has several ways to load an image. If the *same* image was loaded successfully before, and now you could not open correctly, maybe you changed the Preferences. You can check main menu -> File -> Adjust preferences and see if you have set the automatic data conversion options as in the attached pic below.
You can also try to use the Plugins -> ImageIO_Bioformat plugin and import from there. That plugin can read many file formats.
If that does not work (unlikely!), then you can try to load your file first into ImageJ, and then save it to a 3D Tiff format. Then you should be able to open in V3D. This is because sometimes the Zeiss software saves its file using some special tags that are not compatible with other readers.
best wishes,
-hanchuan
--
====================================
Hanchuan Peng, Ph.D.,
Janelia Farm Research Campus
Howard Hughes Medical Institute
19700 Helix Drive,
Ashburn, VA, 20147, USA.
Tel: (+1) 571-209-4156
Fax: (+1) 571-209-4933
Email: pengh@janelia.hhmi.org
* Peng Lab: http://penglab.janelia.org
* V3D lets you explore & understand your
large 3D/4D/5D images a lot easier!
- fast 3D+ image visualization and analysis,
WYSIWYG, and easy plugin interface:
http://penglab.janelia.org/proj/v3d
On 7/22/10 7:43 PM, Dan G wrote:
> Hello,
>
> I have been using V3D for tracing neurons from LSM stacks. I haven't used it for a few weeks and today when I tried to load an LSM stack I couldn't see anything in the image window. It was just black in every section. The button for viewing in 3D is not available (grayed out), and the only color channels I can select are RGB(all), Red (Chan 1), and Colormap (for indexed image). When I drag the LSM file into the V3D window the Colormap button is selected. Changing the color channel doesn't do anything.
>
> Do you know what's wrong? The image stacks I used to use no longer load either, so I feel like it is probably a setting within V3D that has changed. Also, I downloaded the most recent version to see if that would help, but it did not.
>
> I have attached a screenshot of what I'm seeing. Any help you can offer would be great.
>
> Thanks,
>
> Dan G
V3D has several ways to load an image. If the *same* image was loaded successfully before, and now you could not open correctly, maybe you changed the Preferences. You can check main menu -> File -> Adjust preferences and see if you have set the automatic data conversion options as in the attached pic below.
You can also try to use the Plugins -> ImageIO_Bioformat plugin and import from there. That plugin can read many file formats.
If that does not work (unlikely!), then you can try to load your file first into ImageJ, and then save it to a 3D Tiff format. Then you should be able to open in V3D. This is because sometimes the Zeiss software saves its file using some special tags that are not compatible with other readers.
best wishes,
-hanchuan
--
====================================
Hanchuan Peng, Ph.D.,
Janelia Farm Research Campus
Howard Hughes Medical Institute
19700 Helix Drive,
Ashburn, VA, 20147, USA.
Tel: (+1) 571-209-4156
Fax: (+1) 571-209-4933
Email: pengh@janelia.hhmi.org
* Peng Lab: http://penglab.janelia.org
* V3D lets you explore & understand your
large 3D/4D/5D images a lot easier!
- fast 3D+ image visualization and analysis,
WYSIWYG, and easy plugin interface:
http://penglab.janelia.org/proj/v3d
On 7/22/10 7:43 PM, Dan G wrote:
> Hello,
>
> I have been using V3D for tracing neurons from LSM stacks. I haven't used it for a few weeks and today when I tried to load an LSM stack I couldn't see anything in the image window. It was just black in every section. The button for viewing in 3D is not available (grayed out), and the only color channels I can select are RGB(all), Red (Chan 1), and Colormap (for indexed image). When I drag the LSM file into the V3D window the Colormap button is selected. Changing the color channel doesn't do anything.
>
> Do you know what's wrong? The image stacks I used to use no longer load either, so I feel like it is probably a setting within V3D that has changed. Also, I downloaded the most recent version to see if that would help, but it did not.
>
> I have attached a screenshot of what I'm seeing. Any help you can offer would be great.
>
> Thanks,
>
> Dan G