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Applied Systems Biology - HKI Jena, Germany (@applied-systems-biology)

applied-systems-biology

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Location 🇩🇪 Germany
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jipipe

Java Image Processing Pipeline (JIPipe) is a graphical batch processing language for the ImageJ ecosystem

Dynamic_SPHARM

Software for dynamic spherical harmonic analysis

DeconvTest

A python-based simulation framework that allows the user to quantify and compare the performance of different deconvolution methods.

Jupyter Notebook

misa-framework

Website & downloads repository of MISA++

HelperLib

Helper functions for working with files and parallel processing

amit

This framework allows the segmentation, classification and tracking of immune cells such as PMNs or macrophages and fungal cells in migration and confrontation assays

python3-snakemake-segment-glomeruli

Python 3 snakemake implementation of the glomeruli segmentation algorithm published by Klingberg et al. 2017

cell-migration-simulator

A dynamic cell migration model which is able to simulate dynamic shape changes and migration of motile cells. Developed Marco Blickensdorf from the Research Group Applied Systems Biology headed by Prof. Dr. Marc Thilo Figge at Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Insitute (HKI).

sheepfat

IMFSegNet: cost-effective and objective quantification of intramuscular fat in histological sections by deep learning

Jupyter Notebook