Software Open Access

pyMarAI: nnU-Net-based Tumor Spheroids Auto Delineation

Maus, Jens; Nitschke, Janina; Nikulin, Pavel; Hofheinz, Frank; Barth, Mareike; Lemm, Sandy; Richter, Lena; Pietzsch, Jens; Braune, Anja; Ullrich, Martin

MARC21 XML Export

<?xml version='1.0' encoding='UTF-8'?>
<record xmlns="http://www.loc.gov/MARC21/slim">
  <leader>00000nmm##2200000uu#4500</leader>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">user-health</subfield>
  </datafield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">user-hzdr</subfield>
  </datafield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">user-pet-center</subfield>
  </datafield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">user-rodare</subfield>
  </datafield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">user-zrt</subfield>
  </datafield>
  <datafield tag="520" ind1=" " ind2=" ">
    <subfield code="a">&lt;p&gt;Collection of neural network models for automatic image segmentation of microscopic tumor spheroids. Intended to be used with nnU-Net deep-learning framework. Trained and tested on a total of microscopic images of mouse pheochromocytoma (MPC) tumor cells.&lt;/p&gt;

&lt;p&gt;In addition to the trained network model, a PyQt5-based graphical user interface tool is provided. This tool provides a complete pipeline for handling microscopic spheroid image data, running deep-learning&amp;ndash;based delineation, and curating results for continuous model improvement.&lt;/p&gt;

&lt;p&gt;For installation and usage instructions, please visit &lt;a href="https://github.com/hzdr-MedImaging/pyMarAI"&gt;https://github.com/hzdr-MedImaging/pyMarAI&lt;/a&gt;&lt;/p&gt;

&lt;p&gt;Please cite&amp;nbsp;&lt;a href="https://www.nature.com/articles/s41592-020-01008-z"&gt;nnU-Net&lt;/a&gt;&amp;nbsp;and the respective paper when using pyMarAI.&lt;/p&gt;

&lt;p&gt;List of available model types:&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;&lt;code&gt;pyMarAI-1.0.0-ecat.zip&lt;/code&gt;: nnUNetv2 ready network (for ECAT7)&lt;/li&gt;
	&lt;li&gt;&lt;code&gt;pyMarAI-1.0.0-nifti.zip&lt;/code&gt;: nnUNetv2 ready network (for NIFTI)&lt;/li&gt;
&lt;/ul&gt;</subfield>
  </datafield>
  <datafield tag="909" ind1="C" ind2="O">
    <subfield code="o">oai:rodare.hzdr.de:4199</subfield>
    <subfield code="p">software</subfield>
    <subfield code="p">user-health</subfield>
    <subfield code="p">user-hzdr</subfield>
    <subfield code="p">user-pet-center</subfield>
    <subfield code="p">user-rodare</subfield>
    <subfield code="p">user-zrt</subfield>
  </datafield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">software</subfield>
  </datafield>
  <datafield tag="540" ind1=" " ind2=" ">
    <subfield code="u">https://creativecommons.org/licenses/by-sa/4.0/legalcode</subfield>
    <subfield code="a">Creative Commons Attribution Share Alike 4.0 International</subfield>
  </datafield>
  <datafield tag="245" ind1=" " ind2=" ">
    <subfield code="a">pyMarAI: nnU-Net-based Tumor Spheroids Auto Delineation</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">Tumor Spheroid Imaging</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">Radiopharmacological Treatment Response Assays</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">Delineation</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">Cancer</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">Deep-Learning</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">Artifical Intelligence</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">Convolutional Neural Networks</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">Network model</subfield>
  </datafield>
  <datafield tag="542" ind1=" " ind2=" ">
    <subfield code="l">open</subfield>
  </datafield>
  <datafield tag="024" ind1=" " ind2=" ">
    <subfield code="a">10.14278/rodare.4199</subfield>
    <subfield code="2">doi</subfield>
  </datafield>
  <datafield tag="773" ind1=" " ind2=" ">
    <subfield code="a">https://www.hzdr.de/publications/Publ-42498</subfield>
    <subfield code="i">isIdenticalTo</subfield>
    <subfield code="n">url</subfield>
  </datafield>
  <datafield tag="773" ind1=" " ind2=" ">
    <subfield code="a">https://www.hzdr.de/publications/Publ-42497</subfield>
    <subfield code="i">isReferencedBy</subfield>
    <subfield code="n">url</subfield>
  </datafield>
  <datafield tag="773" ind1=" " ind2=" ">
    <subfield code="a">https://github.com/hzdr-MedImaging/pyMarAI</subfield>
    <subfield code="i">isSupplementTo</subfield>
    <subfield code="n">url</subfield>
  </datafield>
  <datafield tag="773" ind1=" " ind2=" ">
    <subfield code="a">10.14278/rodare.4198</subfield>
    <subfield code="i">isVersionOf</subfield>
    <subfield code="n">doi</subfield>
  </datafield>
  <controlfield tag="001">4199</controlfield>
  <datafield tag="100" ind1=" " ind2=" ">
    <subfield code="a">Maus, Jens</subfield>
    <subfield code="0">(orcid)0000-0002-7195-9927</subfield>
  </datafield>
  <controlfield tag="005">20260107152139.0</controlfield>
  <datafield tag="260" ind1=" " ind2=" ">
    <subfield code="c">2026-01-07</subfield>
  </datafield>
  <datafield tag="650" ind1="1" ind2="7">
    <subfield code="a">cc-by</subfield>
    <subfield code="2">opendefinition.org</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="a">Nitschke, Janina</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="a">Nikulin, Pavel</subfield>
    <subfield code="0">(orcid)0000-0002-4568-4018</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="a">Hofheinz, Frank</subfield>
    <subfield code="0">(orcid)0000-0001-8016-4643</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="a">Barth, Mareike</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="a">Lemm, Sandy</subfield>
    <subfield code="0">(orcid)0000-0001-6763-5957</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="a">Richter, Lena</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="a">Pietzsch, Jens</subfield>
    <subfield code="0">(orcid)0000-0002-1610-1493</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="a">Braune, Anja</subfield>
    <subfield code="0">(orcid)0000-0001-7707-9413</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="a">Ullrich, Martin</subfield>
    <subfield code="0">(orcid)0000-0001-6104-6676</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">771346916</subfield>
    <subfield code="u">https://rodare.hzdr.de/record/4199/files/pyMarAI-1.0.0-ecat.zip</subfield>
    <subfield code="z">md5:080c71677fa8fb76699c0fe0fa7b6055</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">771346936</subfield>
    <subfield code="u">https://rodare.hzdr.de/record/4199/files/pyMarAI-1.0.0-nifti.zip</subfield>
    <subfield code="z">md5:fb5bbfab30e23c77542a2fd1eb82132e</subfield>
  </datafield>
</record>
109
1
views
downloads
All versions This version
Views 109109
Downloads 11
Data volume 771.3 MB771.3 MB
Unique views 104104
Unique downloads 11
More info on how stats are collected.
Available in
Publication date:
January 7, 2026
DOI:
10.14278/rodare.4199

RODARE DOI Badge

DOI 

10.14278/rodare.4199

Markdown 

[![DOI](https://rodare.hzdr.de/badge/DOI/10.14278/rodare.4199.svg)](https://doi.org/10.14278/rodare.4199)

reStructedText 

.. image:: https://rodare.hzdr.de/badge/DOI/10.14278/rodare.4199.svg
   :target: https://doi.org/10.14278/rodare.4199

HTML 

<a href="https://doi.org/10.14278/rodare.4199"><img src="https://rodare.hzdr.de/badge/DOI/10.14278/rodare.4199.svg" alt="DOI"></a>

Image URL 

https://rodare.hzdr.de/badge/DOI/10.14278/rodare.4199.svg

Target URL 

https://doi.org/10.14278/rodare.4199

Keyword(s):
Tumor Spheroid Imaging Radiopharmacological Treatment Response Assays Delineation Cancer Deep-Learning Artifical Intelligence Convolutional Neural Networks Network model
Related identifiers:
Identical to:
https://www.hzdr.de/publications/Publ-42498
Referenced by:
https://www.hzdr.de/publications/Publ-42497
Supplement to:
https://github.com/hzdr-MedImaging/pyMarAI
Communities:
License (for files):
Creative Commons Attribution Share Alike 4.0 International

Versions

Version 1.0.0 10.14278/rodare.4199 Jan 7, 2026
Cite all versions? You can cite all versions by using the DOI 10.14278/rodare.4198. This DOI represents all versions, and will always resolve to the latest one. Read more.

Share

Cite as

Export