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. 2023 Jul 12;24(1):283.
doi: 10.1186/s12859-023-05403-z.

VolumePeeler: a novel FIJI plugin for geometric tissue peeling to improve visualization and quantification of 3D image stacks

Marilyn Gatica  1 , Carlos F Navarro  2   3 , Alejandro Lavado  2   3 , German Reig  4 , Eduardo Pulgar  5 , Paula Llanos  6 , Steffen Härtel  2   3   7 , Andrea Ravasio  8 , Cristina Bertocchi  9   10 , Miguel L Concha  2   3   11 , Mauricio Cerda  12   13   14   15
Affiliations

VolumePeeler: a novel FIJI plugin for geometric tissue peeling to improve visualization and quantification of 3D image stacks

Marilyn Gatica et al. BMC Bioinformatics. .

Abstract

Motivation: Quantitative descriptions of multi-cellular structures from optical microscopy imaging are prime to understand the variety of three-dimensional (3D) shapes in living organisms. Experimental models of vertebrates, invertebrates and plants, such as zebrafish, killifish, Drosophila or Marchantia, mainly comprise multilayer tissues, and even if microscopes can reach the needed depth, their geometry hinders the selection and subsequent analysis of the optical volumes of interest. Computational tools to "peel" tissues by removing specific layers and reducing 3D volume into planar images, can critically improve visualization and analysis.

Results: We developed VolumePeeler, a versatile FIJI plugin for virtual 3D "peeling" of image stacks. The plugin implements spherical and spline surface projections. We applied VolumePeeler to perform peeling in 3D images of spherical embryos, as well as non-spherical tissue layers. The produced images improve the 3D volume visualization and enable analysis and quantification of geometrically challenging microscopy datasets.

Availability: ImageJ/FIJI software, source code, examples, and tutorials are openly available in https://cimt.uchile.cl/mcerda.

Keywords: 3D projections; Image processing; Microscopy; Virtual 3D peeling.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
For the two available Spherical (a) and Spline (b) surface projections in VolumePeler, user parameter options (first row), and volume peeling options (second row) are depicted
Fig. 2
Fig. 2
a Synthetic test volume. b VolumePeeler (proposed, RMSE=20.54), LocalZProjector (RMSE=18.09, time=20 [s]), and Max. Intensity (RMSE=23.1, time<1 [s]) projections applied to the synthetic volume. VolumePeeler was set to retrieve upper plane. c VolumePeeler is the only method that can be set to retrieve lower gray plane (RMSE=197.87)
Fig. 3
Fig. 3
Three application examples of VolumePeeler: a Killifish, b Zebrafish, and c Marchantia tissue. In each example the stack (first row), 2D projections from VolumePeeler and Max. Intensity (second row), and 3D views (third row) are shown. Further comparisons with LocalZProjector are provided in Additional file 1: Fig. 2
See this image and copyright information in PMC

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