Problem with Bioformats Plugin

Tags: #<Tag:0x00007fd54289ebe8> #<Tag:0x00007fd54289fd18> #<Tag:0x00007fd54289fac0>


I have been remeshing 3D surfaces in AMIRA to decrease memory size; however, when viewing the surface in Fiji 3D viewer, an exception error popped up and I got this error below. I am using the Import/Show Amira Surface plugin andI am not sure what it means; I am only running into this error with remeshed (.surf) 3D surfaces.

(Fiji Is Just) ImageJ 2.0.0-rc-59/1.51k; Java 1.8.0_66 [64-bit]; Mac OS X 10.11.6; 74MB of 96MB (76%)


I have used other softwares to view the remeshed surfaces and have confirmed with AMIRA that the remeshed surfaces seem to be fine, but the problem lies with the way they are being read with the Show Amira Surface Plugin. If you export the remeshed surface to .PLY, reload into Amira, then export as .SURF, the resulting file can be displayed in Fiji, but a little strangely. It’s if there are two surfaces – one gray, that includes all materials, and another that consists of each material separately.

I have tried importing using the bioformats menu plugin as well and got this error:

loci.formats.UnknownFormatException: Unknown file format: /Users/labadmin/Desktop/From confocal/Image Expt#4_WT_Chi_col1a1 GFP_sp7mCherry/3D Labels and Reconstruction/
	at loci.formats.ImageReader.getReader(
	at ij.IJ.runUserPlugIn(
	at ij.IJ.runPlugIn(
	at ij.Executer.runCommand(

The behavior of this plugin does not seem to be normal, are there any ImageJ developers that could help with this problem?



3D viewer doesnt support “.surf” files. Try resaving your mesh as “.stl” or “.obj” both of which 3D viewer can read.

Note that at the moment bioformats doesn’t handle any meshes. The importing of meshes is entirely handled by 3D viewer, and in the future some upcoming tools.

I see the bit about the Amira plugin (which I haven’t used). However, I still suggest giving stl’s or obj’s (and using 3D viewer) a try.


hi @kephale,

Thanks for your response. Saving the mesh as .stl or .obj has been successful for me to convert to .u3d using MeVisLab; however, these formats do not retain the model tree information i.e structure labels. I have successfully imported the entire structure in Adobe, but without the labeling information. I run into weird errors when importing .stl or .ply using Bioformats with my remeshed and non-remeshed data.

With the Show Amira Surface plugin, the .surf file is imported into Fiji and 3D viewer opens up automatically to display the .surf file. I could then interact with the 3D viewer and could export the surface as .u3d.


Aha! Well, unfortunately I don’t have a useful suggestion. However, I have added labeled mesh data a la .surf to the wishlist for the upcoming threedviewer.


This plugin is part of the VIB collection:

Unfortunately, both people involved in its development have ceased maintaining it. So I fear you are on your own with respect to troubleshooting it.