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List of works by Tim Wilhelm Nattkemper

A Normalized Tree Index for identification of correlated clinical parameters in microarray experiments

scientific article

A Novel Methodology for Characterizing Cell Subpopulations in Automated Time-lapse Microscopy

scientific article

A Tree Index to Support Clustering Based Exploratory Data Analysis

A Web2.0 Strategy for the Collaborative Analysis of Complex Bioimages

A computer vision approach for monitoring the spatial and temporal shrimp distribution at the LoVe observatory

scholarly article published April 2016

A guide through the computational analysis of isotope-labeled mass spectrometry-based quantitative proteomics data: an application study

scientific article

A machine vision system for automated non-invasive assessment of cell viability via dark field microscopy, wavelet feature selection and classification

scientific article

A method for linking computed image features to histological semantics in neuropathology

scientific article published on 05 July 2007

A neural classifier enabling high-throughput topological analysis of lymphocytes in tissue sections.

scientific article published in June 2001

A neural network architecture for automatic segmentation of fluorescence micrographs

article by Tim W. Nattkemper et al published October 2002 in Neurocomputing

A rapid reporter system using GFP as a reporter protein for identification and screening of synthetic stationary-phase promoters in Escherichia coli

scientific article published on 13 July 2005

A way toward analyzing high-content bioimage data by means of semantic annotation and visual data mining

AKE - the Accelerated k-mer Exploration web-tool for rapid taxonomic classification and visualization

scientific article

ALLocator: an interactive web platform for the analysis of metabolomic LC-ESI-MS datasets, enabling semi-automated, user-revised compound annotation and mass isotopomer ratio analysis

scientific article

An adaptive tissue characterization network for model-free visualization of dynamic contrast-enhanced magnetic resonance image data

scientific article

An in situ probe for on-line monitoring of cell density and viability on the basis of dark field microscopy in conjunction with image processing and supervised machine learning.

scientific article

Analysis of breast MRI data based on (topographic) independent and tree-dependent component analysis

Approaches to automatic parameter fitting in a microscopy image segmentation pipeline: An exploratory parameter space analysis

scientific article published on 30 March 2013

Automated detection and quantification of fluorescently labeled synapses in murine brain tissue sections for high throughput applications.

scientific article

Automatic Recognition of Muscle-Invasive T-Lymphocytes Expressing Dipeptidyl-Peptidase IV (CD26) and Analysis of the Associated Cell Surface Phenotypes

Automatic segmentation of digital micrographs: a survey.

scientific article published on January 2004

BIIGLE 2.0 - Browsing and Annotating Large Marine Image Collections

BIIGLE Tools – A Web 2.0 Approach for Visual Bioimage Database Mining

Biigle - Web 2.0 enabled labelling and exploring of images from the Arctic deep-sea observatory HAUSGARTEN

BioIMAX: a Web 2.0 approach for easy exploratory and collaborative access to multivariate bioimage data

scientific article

BioImaging: Contributions from biology, physics and informatics

scientific article published on 01 September 2010

Breast MRI data analysis by LLE

Categorization of two-photon microscopy images of human cartilage into states of osteoarthritis

scientific article

CellViCAM--Cell viability classification for animal cell cultures using dark field micrographs

scientific article published on 23 July 2010

Comparison of Acceleration Techniques for Selected Low-Level Bioinformatics Operations.

scientific article

Comparison of image annotation data generated by multiple investigators for benthic ecology

scientific article published in 2016

Computational Visual Stress Level Analysis of Calcareous Algae Exposed to Sedimentation

scientific article

Computational coral feature monitoring for the fixed underwater observatory LoVe

scholarly article published September 2016

Computer vision enables short- and long-term analysis of Lophelia pertusa polyp behaviour and colour from an underwater observatory

scientific article published on 29 April 2019

Construction of a large signature-tagged mini-Tn5 transposon library and its application to mutagenesis of Sinorhizobium meliloti

scientific article published in June 2006

Current Trends and Future Directions of Large Scale Image and Video Annotation: Observations From Four Years of BIIGLE 2.0

scientific article published in 2021

Current and future trends in marine image annotation software

scientific article published in December 2016

DELPHI—fast and adaptive computational laser point detection and visual footprint quantification for arbitrary underwater image collections

Data storage and data re-use in taxonomy—the need for improved storage and accessibility of heterogeneous data

scientific article published on 20 January 2020

Deep learning-based diatom taxonomy on virtual slides

scientific article published on 02 September 2020

Detection and visualization of communities in mass spectrometry imaging data.

scientific article published on 4 June 2019

Detection of Focal Cortical Dysplasia Lesions in MRI Using Textural Features

Detection of suspicious lesions in dynamic contrast enhanced MRI data

scientific article

Evaluation of radiological features for breast tumour classification in clinical screening with machine learning methods.

scientific article

Feature-space exploration of pathology images using content-based database visualization

scholarly article published 2 March 2006

Flexible synapse detection in fluorescence micrographs by modeling human expert grading

Fully automated image segmentation for benthic resource assessment of poly-metallic nodules

scholarly article by Timm Schoening published in April 2016

Fusing Biomedical Multi-modal Data for Exploratory Data Analysis

GISMO--gene identification using a support vector machine for ORF classification

scientific article published on 14 December 2006

Histologic characterization of DCE-MRI breast tumors with dimensional data reduction

Human vs machine: evaluation of fluorescence micrographs.

scientific article

Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification.

scientific article published on 5 June 2008

ISOLLE: LLE with geodesic distance

ISOLLE: Locally Linear Embedding with Geodesic Distance

Identification of Genes Relevant to Symbiosis and Competitiveness in Sinorhizobium meliloti Using Signature-Tagged Mutants

article

Image Fusion Based on Topographic Mappings Using the Hyperbolic Space

Image analysis-based quantification of fungal sporulation by automatic conidia counting and gray value correlation

scientific article published on 07 January 2021

Image fusion for dynamic contrast enhanced magnetic resonance imaging

scientific article

Improved Mass Spectrometry Peak Intensity Prediction by Adaptive Feature Weighting

In situ dark field microscopy for on-line monitoring of yeast cultures

scientific article

Integrating semantic annotation and information visualization for the analysis of multichannel fluorescence micrographs from pancreatic tissue.

scientific article published on 06 December 2009

Investigation of hidden parameters influencing the automated object detection in images from the deep seafloor of the HAUSGARTEN observatory

Learning to Classify Organic and Conventional Wheat - A Machine Learning Driven Approach Using the MeltDB 2.0 Metabolomics Analysis Platform.

scientific article published on 24 March 2015

Libraries of synthetic stationary-phase and stress promoters as a tool for fine-tuning of expression of recombinant proteins in Escherichia coli.

scientific article

Look & listen: sonification and visualization of multiparameter micrographs

article

Looking inside self-organizing map ensembles with resampling and negative correlation learning.

scientific article published on 27 August 2010

MAIA-A machine learning assisted image annotation method for environmental monitoring and exploration

scientific article published in PLoS ONE

Machine learning approaches for phenotype-genotype mapping: predicting heterozygous mutations in the CYP21B gene from steroid profiles

scientific article

Making marine image data FAIR

scientific article published in 2022

Megafauna community assessment of polymetallic-nodule fields with cameras: platform and methodology comparison

scientific article published in 2020

Megafaunal assemblages from two shelf stations west of Svalbard

scientific article published in 2011

MeltDB 2.0-advances of the metabolomics software system

scientific article

MetHoS: a platform for large-scale processing, storage and analysis of metabolomics data

scientific article published on 08 July 2022

Microhabitat and shrimp abundance within a Norwegian cold-water coral ecosystem

scientific article published in 2013

Model-Free Visualization of Suspicious Lesions in Breast MRI Based on Supervised and Unsupervised Learning

scientific article published on March 2008

Multiscale analysis of MR-mammography data.

scientific article

Multiscale entropy analysis in dynamic contrast-enhanced MRI

Multivariate image analysis in biomedicine.

scientific article published in October 2004

Multivariate image mining

Neural Network Approach for Mass Spectrometry Prediction by Peptide Prototyping

Omics Fusion - A Platform for Integrative Analysis of Omics Data

scientific article

On the application of (topographic) independent and tree-dependent component analysis for the examination of DCE-MRI data

scientific article

On the impact of Citizen Science-derived data quality on deep learning based classification in marine images

scientific article published in 2019

PEAK INTENSITY PREDICTION FOR PMF MASS SPECTRA USING SUPPORT VECTOR REGRESSION

Peak intensity prediction in MALDI-TOF mass spectrometry: a machine learning study to support quantitative proteomics

scientific article

Perspectives In Visual Imaging for Marine Biology and Ecology: From Acquisition to Understanding

article published in 2016

Phylogenetic classification of short environmental DNA fragments

scientific article (publication date: April 2008)

Polyp Activity Estimation and Monitoring for Cold Water Corals with a Deep Learning Approach

scholarly article published December 2016

Protein turnover quantification in a multilabeling approach: from data calculation to evaluation

scientific article

Quantification of cell infection caused by Listeria monocytogenes invasion.

scientific article

Qupe--a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments

scientific article published on 6 October 2009

RAMTaB: robust alignment of multi-tag bioimages.

scientific article

Ranking Color Correction Algorithms Using Cluster Indices

scholarly article published August 2014

Re-expression of IGF-II is important for beta cell regeneration in adult mice

scientific article

Reagent-free automatic cell viability determination using neural networks based machine vision and dark-field microscopy in Saccharomyces cerevisiae

scientific article

RecoMIA—Recommendations for Marine Image Annotation: Lessons Learned and Future Directions

article published in 2016

Report on the Marine Imaging Workshop 2022

scientific article published on 18 March 2024

Repositories for Taxonomic Data: Where We Are and What is Missing

scientific article published on 16 April 2020

Robust normalization protocols for multiplexed fluorescence bioimage analysis.

scientific article published on 5 March 2016

SOM-Based Wavelet Filtering for the Exploration of Medical Images

scholarly article by Birgit Lessmann et al published 2005 in Lecture Notes in Computer Science

Seabed Classification Using a Bag-of-Prototypes Feature Representation

SeeVis - 3D space-time cube rendering for visualization of microfluidics image data

scholarly article by Georges Hattab & Tim W Nattkemper published 22 October 2018 in Computer applications in the biosciences : CABIOS

Semi-automated image analysis for the assessment of megafaunal densities at the Arctic deep-sea observatory HAUSGARTEN.

scientific article

Spatio-Temporal Metabolite Profiling of the Barley Germination Process by MALDI MS Imaging

scientific article

TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach

scientific article

The Diversity of Regression Ensembles Combining Bagging and Random Subspace Method

The Impact of Data Augmentations on Deep Learning-Based Marine Object Classification in Benthic Image Transects

scientific article published in 2022

The quest for seafloor macrolitter: a critical review of background knowledge, current methods and future prospects

Towards Improved Epilepsia Diagnosis by Unsupervised Segmentation of Neuropathology Tissue Sections using Ripley’s- $${\rm{\hat L}}$$ Features

Tumor feature visualization with unsupervised learning.

scientific article published in August 2005

Use of machine-learning algorithms for the automated detection of cold-water coral habitats: a pilot study

scholarly article by A Purser et al published 17 December 2009 in Marine Ecology Progress Series

ViCAR: An Adaptive and Landmark-Free Registration of Time Lapse Image Data from Microfluidics Experiments

scientific article

Visual exploratory analysis of DCE-MRI data in breast cancer by dimensional data reduction: A comparative study

article published in 2006

Visualization of multivariate image data using image fusion and perceptually optimized color scales based on sRGB

scholarly article published 5 May 2004

Visualization of suspicious lesions in breast MRI based on intelligent neural systems

scholarly article published 5 May 2006

WHIDE--a web tool for visual data mining colocation patterns in multivariate bioimages

scientific article

Web2.0 paves new ways for collaborative and exploratory analysis of chemical compounds in spectrometry data

scientific article

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