Isotropic Reconstruction (Zebrafish retina)


This work (method and data) is part of Content-aware image restoration: pushing the limits of fluorescence microscopy by Martin Weigert et al. in Nature Methods.


In contrast to previous examples, isotropic volumes that could be used as input/ground-truth training pairs are not readily obtainable. Therefore we propose to compute realistic observations from real ground-truth image data in-silico.

We applied this approach to 10-fold undersampled acquisitions of the developing retina of Danio rerio (zebrafish) embryos and observed that the trained CARE Network reconstructed isometric image data.


The trained model is published for demonstration purposes. You can try it via Fiji and KNIME.

To run the demo in Fiji, follow these instructions.

To run the demo in KNIME, follow these instructions.


Using CARE to computationally increase axial resolution of an imaged zebrafish retina to de-facto isometric resolution.