MPI-CBG ZibAmira Portal

Automated tracing of microtubules in plastic-embedded electron tomograms

* This service is offered for non-commercial research purposes only *


This portal provides an image processing service for academia / research in cell biology. The purpose is to demonstrate automated tracing of microtubules from 3D image stacks obtained from electron tomography.

This was developed as part of a research project on the organization of microtubules in C.elegans embryo ([1]). The service is offered for non-commercial research purposes only, without warranty that it will produce the expected result. However, limited support can be obtained by contacting and feedback is welcome.
Electron tomograms can be submitted on line using the "Processing Task Subscription Form" below.


The 3D stacks must be in the MRC format([2]) as obtained by reconstruction of electron tomograms using the IMOD software ([3], [4] and link to imod) for example.

The missing wedge parameters used are assuming that the data come from dual-tilt tomography with an angular range close to ±60°. The data needs to be 32-bit real or byte (8-bits) (MRC mode 0 or 2). The contrast of 8 bit images needs to be adjusted to fit the 8-bit range as good as possible. The file size is limited to 10 GB. The tracing software will use the pixel size from the MRC file. This information is required. It was tested with pixel sizes up to 4nm. If you need more detailed explanation of the requirements, please, click more.


Please fill the form below. The email address is mandatory, it will be used to send you a link to the result data and to inform you when the process is completed.

Before sending big files, please note that the time of file upload is heavily dependent on the file size and available bandwidth. We cannot guarantee a bandwidth for this system as it depends on the load of our servers and on end-user internet connection. The IMOD file will be checked upon arrival for a pixel size between 10 to 50 Angstroms. If it does not comply, it will not be processed. Upon job completion, you will receive an e-mail stating the location of the results. Note, that your data (maximum size: 10 GB) will be deleted 14 days after submission.

Processing Task Submission Form

Description * Task description should be given here.
Filename * The file size should be less than 1500 MB.

* This service is offered for non-commercial research purposes only *