Reconstructing large volumetric microscopy for analysis, visualization and 3D printing with Paintera

Reconstructing large volumetric microscopy for analysis, visualization, and 3D printing with Paintera and Blender | Caleb Hulbert, Igor Siwanowicz | November 18th, Halfway to I2K 2025 Authors: Caleb Hulbert, Janelia; Igor Siwanowicz Janelia Workshop Description: Paintera is a JavaFX-based annotation software designed for dense labeling of arbitrarily large 3D volumetric data from microscopy. Paintera's core capabilities include 2D painting and 3D shape interpolation in virtual slices at arbitrary orientations, multi-scale handling of both raw data and labels, and on-the-fly multi-scale mesh generation with adaptive level of detail. Segmentations can be exported as meshes and further refined Blender. Paintera supports local and remote datasets in N5, Zarr, or HDF5 format, and is built on the Imglib2 and BigDataViewer libraries. Target Audience: Beginner users, intermediate users Keywords: 3D annotation, dense labeling, mesh generation, Segment Anything, SAM, arbitrary reslicing, multi-scale, N5, Zarr, HDF5, JavaFX, volume segmentation, shape interpolation, adaptive level of detail, connectomics, proofreading, Imglib2, BigDataViewer