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MR. Johannes Seiffarth

Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich

I am interested in the analysis of image modalities with special interest on machine learning and analysis workflows.

Helmholtz Imaging Projects

2020: SATOMI - Tackling the segmentation and tracking challenges of growing colonies and microbial diversity

Send mail to Johannes Seiffarth (j.seiffarth@fz-juelich.de)

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Forschungszentrum Jülich - Jülich/Cologne

Johannes Seiffarth in Helmholtz Imaging CONNECT:

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Center

Forschungszentrum Jülich (FZJ)

Forschungszentrum Jülich is a large-scale national research facility in the Helmholtz Association of German Research Centres. By conducting research on the global challenges currently facing society, we contribute to the welfare of mankind and responsible …

In Helmholtz Imaging CONNECT
➤Applications: 52 ➤Facilities: 3 ➤Instruments: 23 ➤Labs: 16 ➤Modalities: 65 ➤Experts: 21 ➤Solutions: 6

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Solution

CellSium - Versatile Cell Simulator for Microcolony Ground Truth Generation

To train deep learning-based segmentation models, large ground truth datasets are needed. To address this need in microfluidic live-cell imaging, we developed CellSium, a flexibly configurable cell simulator built to synthesize realistic image sequences of …

In Helmholtz Imaging CONNECT
➤Applications: 0 ➤Facilities: 0 ➤Centers: 0 ➤Instruments: 0 ➤Labs: 0 ➤Modalities: 0 ➤Experts: 2

Solution

MicrobeSEG: A deep learning software tool with OMERO data management for efficient and accurate cell segmentation (microbeSEG)

microbeSEG is a deep learning-based tool for instance segmentation of roundish objects in 2D and 2D+t data, e.g., microbes. The microbeSEG workflow covers training data creation (with pre-labeling) or import, model training, model evaluation, and …

In Helmholtz Imaging CONNECT
➤Applications: 7 ➤Facilities: 0 ➤Centers: 2 ➤Instruments: 0 ➤Labs: 0 ➤Modalities: 0 ➤Experts: 4

Solution

ObiWan-Microbi: OMERO-based integrated workflow for annotating microbes in the cloud (ObiWan-Microbi)

ObiWan-Microbi: OMERO-based integrated Workflow for annotating Microbes in the Cloud

Preview

ObiWan-Microbi is a toolkit collection for semi-automated segmentation and annotation of (biological) time-lapse image data in the cloud. It utilizes an OMERO image server for …

In Helmholtz Imaging CONNECT
➤Applications: 5 ➤Facilities: 0 ➤Centers: 2 ➤Instruments: 2 ➤Labs: 0 ➤Modalities: 4 ➤Experts: 1