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

Important Information:

for motors replacement reasons on our air conditioning,

the BIOP will be closed and inaccessible during the entire week,

from Monday August 29th  till Friday September 2nd .

Sorry for the inconvenience.

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

Transfering registration from different modalities, here fluorescence to brightfield

Whole Slide Registration Workflow Published

Our very own Nicolas has recently published a new article in Frontiers entitled: “An Open-Source Whole Slide Image Registration Workflow at Cellular Precision Using Fiji, QuPath and Elastix”

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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