Create an order

Register an account to access 3dEMtrace. Then simply select which cell structure(s) you want to segment.

We currently provide segmentation services for these cell structures:

  • Nuclei

  • Mitochondria

  • Endoplasmic

  • Synaptic

Upload a dataset

You can upload a ZIP or TIFF file (up to 60 GiB) for every dataset. You can also upload annotated images or a PDF document for any additional information that could be helpful for processing your data.

Click the “Start Analysis” button to start the segmentation. Then lean back and let us do the work. You will receive an e-mail notification once your segmentation task has been finished.


The price per dataset is based on which kind of organelles you want to have segmented. You can combine different segmentation categories per submission. A base fee of 1,000 EUR is added per submission (it is only added once).



Endoplasmic reticulum

Synaptic junctions
Category price* 1,000.00 EUR 1,500.00 EUR 2,000.00 EUR 2,000.00 EUR
Base price for each analysis* 1,000.00 EUR
Max. dataset size 60 GiB

*Excluding VAT.


I would like to segment cellular structures that are not on the list or my dataset is larger than 60 GB, what should I do?

We will do our best to satisfy all your segmentation needs. Just contact us at if you would like to segment cellular structures that are not on the list or if your dataset exceeds 60GB.

What payment options do you accept?

We accept VISA cards and MasterCard. Payment is handled via stripe. If you are interested in using 3dEMtrace, but do not have access to a credit card, please contact us at

How are the results delivered?

The segmentation results are provided as TIFF stacks. If you require any other file format, please get in touch with us at

How long does the segmentation take?

Usually, your order will be segmented within 1–2 months. The duration will depend on the dataset quality and the difficulty of the segmentation task. You will be notified by e-mail once your results are ready for download.

What are the browser requirements for the dataset upload?

All modern, standards-confirming browsers should work. Please enable JavaScript in your browser to use the upload interface.

Is my data safe with you?

We take data security very seriously. All data provided by our customers is kept strictly confidential and maintained on secure infrastructure.