Adaptive and Background-Aware GAL4 Expression Enhancement of Co-registered Confocal Microscopy Images


GAL4 gene expression imaging using confocal microscopy is a common and powerful technique used to study the nervous system of a model organism such as Drosophila melanogaster. Recent research projects focused on high throughput screenings of thousands of different driver lines, resulting in large image databases. The amount of data generated makes manual assessment tedious or even impossible. The first and most important step in any automatic image processing and data extraction pipeline is to enhance areas with relevant signal. However, data acquired via high throughput imaging tends to be less then ideal for this task, often showing high amounts of background signal. Furthermore, neuronal structures and in particular thin and elongated projections with a weak staining signal are easily lost. In this paper we present a method for enhancing the relevant signal by utilizing a Hessian-based filter to augment thin and weak tube-like structures in the image. To get optimal results, we present a novel adaptive background-aware enhancement filter parametrized with the local background intensity, which is estimated based on a common background model. We also integrate recent research on adaptive image enhancement into our approach, allowing us to propose an effective solution for known problems present in confocal microscopy images. We provide an evaluation based on annotated image data and compare our results against current state-of-the-art algorithms. The results show that our algorithm clearly outperforms the existing solutions.

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This work was funded by the FFG Headquarter Project “Molecular Basis” grant number 834223. We would like to thank Barry J. Dickson (Janelia Research Campus, USA) and Pawel Pasierbek (Research Institute of Molecular Pathology, Austria) for the image data and their advice. We would also like to thank Anne von Philipsborn (Aarhus University, Denmark) for providing the secondary dataset.

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Correspondence to Florian Schulze.

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Trapp, M., Schulze, F., Novikov, A.A. et al. Adaptive and Background-Aware GAL4 Expression Enhancement of Co-registered Confocal Microscopy Images. Neuroinform 14, 221–233 (2016).

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  • Adaptive image enhancement
  • Background-aware
  • Neuron
  • Confocal microscopy
  • Drosophila
  • GAL4 enhancement
  • BrainGazer