Lif -> Ome.Tif Issue

ome-tiff
fiji
imagej
Tags: #<Tag:0x00007fd542174c50> #<Tag:0x00007fd542174ae8> #<Tag:0x00007fd5421748e0>

#1

Our lab has 3D confocal microscopy data that we want to analyze in AMIRA software. We use ImageJ to convert the file from .lif (from Leica microscope) to universal .ome.tif format. However, after conversion to .ome-tiff format, the z-stack appears to be stretched in the z-axis on ImageJ and AMIRA. Do you have any suggestions on how to solve this problem so we can correctly access the data into AMIRA for further processing and analysis?


Bioformats export as OME.TIFF scale bug
#2

Dear @azmanr,

welcome to the forum! :slight_smile:

To do the conversion, you do not necessarily need ImageJ. Bio-Formats provides command-line tools that you could use instead.

That said, could you describe the issue in more detail and provide example data if possible? In comparison to which visualization do the images appear “stretched”?

Also, some bugs with the LIF format were fixed in a recent version of Bio-Formats (see release notes for details). You might be able to solve your problem by updating your Fiji/ImageJ installation.

Best,
Stefan


#3

Hi @stelfrich,

Thanks for your response. I am using Fiji that updates frequently and contains the Bioformats plugin. Would the command-line tools be more useful? Essentially, my problem is that have .lif files from a Confocal Microscope that I want to bring into Amira. But, I am running into problems with this process. I have been bringing the .lif files into Fiji and converting them to .ome-tiff to be read in Amira for reconstruction analysis. The reconstructions appear fine when I open 3D surface in Fiji for the .lif file. But, when I save the file as .ome-tif, the Fiji reconstruction does not display any recognizable surface. In Amira, the surface appears significantly stretched in the z-axis, even though the voxel information is entered when the file is opened in Amira. When opening the ome-tiff file in Fiji, the voxel information is changed. But even if I go to properties and save the proper voxel information, the reconstruction with the one-tiff file is the same. I am unable to share the .lif or .ome-tif file on this forum, but I can try sending it to you through email.

Thanks,
Azman


#4

Experiment001.lif.zip (25.6 MB)

Attached is a sample lif file in zip format


#5

Ideally, you wouldn’t have to open Fiji to do the conversion, but do it from the command-line instead. But that might be the next step after solving this issue.

Do you mean the menu entry Analyze > 3D Surface Plot?

I have saved the LIF via Plugins > Bio-Formats > Bio-Formats Exporter to an OME-TIFF. When I open that OME-TIFF via Plugins > Bio-Formats > Bio-Formats Importer both the OME-XML metadata as well as ImageJ’s image properties are exactly the same when compared to the LIF: