BioImaging and Optics Platform

Cell Segmentation Using Deep Learning and Nearest Neighbor Analysis

Cells segmented using STARDIST Deep learning, within QuPath software.

Dr. Arne Seitz

Our goal is to provide instruments and more importantly expertise to solve challenging (biological) questions with modern light-microscopy. Therefore the BIOP seeks to create a link between life sciences and engineering to investigate jointly these fundamental fields.

Dr. Arne Seitz, Head of PTBIOP

Expertise

Leica SP8 invert microscope

Microscopy

Widefield, Confocal, Spinning Disk, Lightsheet, Superresolution, Lifetime Imaging, Microdissection

Cell Segmentation in ImageJ-Fiji

Image Processing

Workstations, Deconvolution, Deep Learning, Custom Workflows

Highlights

Sars-Cov 2 illustration

Return to normal for BIOP Staff

The BIOP is currently fully staffed and all staff can be reached by email. On-site staff is currently at 80% each day

DEVILS workflow applied to 3 channel lighthseet cleared brain

DEVILS is published in F1000R

Our Software Tool Article “DEVILS: a tool for the visualization of large datasets with a high dynamic range” is available on F1000R

Trainings at the BIOP

Training

in Microscopy and Image Processing

QuPAth Segmentation Results

Teaching

Undergrad and Post Doc Courses

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