Go back     Home Solutions pyMarAI

pyMarAI

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

Keywords: Tumor Spheroid Imaging, Radiopharmacological Treatment Response Assays, Delineation, Cancer, Deep-Learning, Artifical Intelligence, Convolutional Neural Networks, Network model, Graphical User Interface

https://github.com/hzdr-MedImaging/pyMarAI

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.

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–based delineation, and curating results for continuous model improvement.

Publications

Automatic Delineation of Tumor Spheroids in Microscopic Images Using Deep-Learning

Maus J, Nitschke J, Nikulin P, Hofheinz F, Barth M, Lemm S, Richter L, Pietzsch J, Braune A, Ullrich M - ACS Measurement Science Au - 2026

10.1021/acsmeasuresciau.5c00172

pyMarAI: nnU-Net-based Tumor Spheroids Auto Delineation

Maus J, Nitschke J, Nikulin P, Hofheinz F, Barth M, Lemm S, Richter L, Pietzsch J, Braune A, Ullrich M - Rodare - 2026

10.14278/rodare.4198

pyMarAI Image
pyMarAI deep-learning tumor spheroid segmentation overview
©Jens Maus
Weblinks
Git
License
Apache License 2.0, CC-BY-SA-4.0

Other solutions related to PyMarAI in Helmholtz Imaging CONNECT:

Solution
NnU-Net
logo from imported platform Helmholtz RSD

When confronted with a new dataset, the application of AI-based segmentation methods is non-trivial. Substantial manual effort is required to optimize the network topology, preprocessing, training procedure and inference strategy to the task at hand. …

In Helmholtz Imaging CONNECT
➤Applications: 3 ➤Facilities: 0 ➤Centers: 1 ➤Instruments: 18 ➤Labs: 2 ➤Modalities: 10 ➤Experts: 2

PyMarAI in Helmholtz Imaging CONNECT:

Application
Machine Learning (ML)

Machine learning (ML) is a field of study in artificial intelligence concerned with the development and study of statistical algorithms that can learn from data and generalize to unseen data, and thus perform tasks without …
In Helmholtz Imaging CONNECT
➤Facilities: 0 ➤Centers: 6 ➤Instruments: 0 ➤Labs: 2 ➤Modalities: 0 ➤Experts: 8 ➤Solutions: 3
Application
Quantification of microscopy data
In Helmholtz Imaging CONNECT
➤Facilities: 0 ➤Centers: 1 ➤Instruments: 0 ➤Labs: 0 ➤Modalities: 0 ➤Experts: 1 ➤Solutions: 5
No facility found.
Center
Helmholtz-Zentrum Dresden-Rossendorf (HZDR)

The long-term goal of the Helmholtz-Zentrum Dresden-Rossendorf (HZDR) is to conduct cutting-edge research in the areas of energy, health, and matter. Strategic collaborations with both national and international partners allow us to address some of …

In Helmholtz Imaging CONNECT
➤Applications: 46 ➤Facilities: 4 ➤Instruments: 38 ➤Labs: 19 ➤Modalities: 104 ➤Experts: 10 ➤Solutions: 5
No instrument found.
Modality
Bright field imaging

Bright-field microscopy (BF) is the simplest of all the optical microscopy illumination techniques. Sample illumination is transmitted (i.e., illuminated from below and observed from above) white light, and contrast in the image is caused by …

Bright-field microscopy, a method of microscopy in which the object to be observed is located in front of a bright background, called the bright field, which illuminates the microscopic image. In this process, the light …

In Helmholtz Imaging CONNECT
➤Applications: 0 ➤Facilities: 1 ➤Centers: 5 ➤Instruments: 3 ➤Labs: 0 ➤Experts: 4 ➤Solutions: 2
Lab
Department of Positron Emission Tomography

The department's research is addressing multiple aspects of the image data acquisition and processing chain, including, among others, image reconstruction, motion correction, modeling of transport and metabolic processes, quantification of tumor shape irregularities, and statistical …

In Helmholtz Imaging CONNECT
➤Applications: 3 ➤Facilities: 0 ➤Centers: 2 ➤Instruments: 0 ➤Modalities: 3 ➤Experts: 1 ➤Solutions: 1
Lab
Department of Radiopharmaceutical and Chemical Biology

Our efforts focus on biochemistry, biology, imaging, and therapy (theranostics) of malignant solid tumors and metastases, with emphasis placed on melanoma, pheochromocytoma, pancreatic ductal adenocarcinoma, hepatocellular carcinoma and multiple myeloma. The discovery and functional characterization …

In Helmholtz Imaging CONNECT
➤Applications: 0 ➤Facilities: 0 ➤Centers: 2 ➤Instruments: 0 ➤Modalities: 4 ➤Experts: 0 ➤Solutions: 1

Helmholtz Imaging spinning wheel

Please wait, your data is processed