Biology subjects

Bakker, G.-J.

Publications and source records attributed to Bakker, G.-J..

3 recordsLinked to original sources

bioRxiv2022

Multi-site assessment of reproducibility in high-content live cell imaging data

High-content image-based cell phenotyping provides fundamental insights in a broad variety of life science areas. Striving for accurate conclusions and meaningful impact demands high reproducibility standards, even more importantly with the advent of data sharing initiatives. However, the sources and degree of biological and technical variability, and thus the reproducibility and usefulness of meta-analysis of results from live-cell microscopy have not been systematically investigated. Here, using high content data describing features of cell migration and morphology, we determine the sources of variability across different scales, including between laboratories, persons, experiments, technical repeats, cells and time points. Significant technical variability occurred between laboratories, providing low value to direct meta-analysis on the data from different laboratories. However, batch effect removal markedly improved the possibility to combine image-based datasets of perturbation experiments. Thus, reproducible quantitative high-content cell image data and meta-analysis depend on standardized procedures and batch correction applied to studies of perturbation effects.

cell biology↗

bioRxiv2020

Intravital Deep-Tumor Single-Beam 2-, 3- and 4-Photon Microscopy

Three-photon excitation has recently been introduced to perform intravital microscopy in deep, previously inaccessible layers of the brain. The applicability of deep-tissue three-photon excitation in more heterogeneously structured, dense tissue types remains, however, unclear. Here we show that in tumors and bone, high-pulse-energy low-duty-cycle infrared excitation near 1300 and 1700 nm enables two-up to fourfold increased tissue penetration compared to conventional 2-photon excitation. Using a single laser line, simultaneous 2-, 3- and 4-photon processes are effectively induced, enabling the simultaneous detection of blue to far-red fluorescence together with second and third harmonic generation. This enables subcellular resolution at power densities in the focus that are not phototoxic to live cells and without color aberration. Thus, infrared high-pulse-energy low-duty-cycle excitation advances deep intravital microscopy in strongly scattering tissue and, in a single scan, delivers rich multi-parameter datasets from cells and complex organ structures.

cancer biology↗

bioRxiv2019

Community Standards for Open Cell Migration Data

Cell migration research has become a high-content field. However, the quantitative information encapsulated in these complex and high-dimensional datasets is not fully exploited due to the diversity of experimental protocols and non-standardised output formats. In addition, typically the datasets are not open for reuse. Making the data open and Findable, Accessible, Interoperable, and Reusable (FAIR) will enable meta-analysis, data integration, and data mining. Standardised data formats and controlled vocabularies are essential for building a suitable infrastructure for that purpose but are not available in the cell migration domain. We here present standardisation efforts by the Cell Migration Standardisation Organization, CMSO, an open community-driven organisation to facilitate the development of standards for cell migration data. This work will foster the development of improved algorithms and tools, and enable secondary analysis of public datasets, ultimately unlocking new knowledge of the complex biological process of cell migration.

bioinformatics↗