# MiShape: 3D Shape Modelling of Mitochondria in Microscopy

arXiv: https://arxiv.org/abs/2303.01546 · HTML: https://mlsanity.com/paper/2303.01546/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 20 of its 64 references that are in the map.
- First posted on arXiv 2 Mar 2023.

## Builds on (most cited first, 20 of 20)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [EfficientNet: Rethinking Model Scaling for Convolutional Neural Networks](https://mlsanity.com/paper/1905.11946/) (2019)
- [DeepSDF: Learning Continuous Signed Distance Functions for Shape Representation](https://mlsanity.com/paper/1901.05103/) (2019)
- [V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/1606.04797/) (2016)
- [Occupancy Networks: Learning 3D Reconstruction in Function Space](https://mlsanity.com/paper/1812.03828/) (2018)
- [SlowFast Networks for Video Recognition](https://mlsanity.com/paper/1812.03982/) (2018)
- [TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation](https://mlsanity.com/paper/2102.04306/) (2021)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [Learning Implicit Fields for Generative Shape Modeling](https://mlsanity.com/paper/1812.02822/) (2018)
- [UNet++: Redesigning Skip Connections to Exploit Multiscale Features in Image Segmentation](https://mlsanity.com/paper/1912.05074/) (2019)
- [Learning a Probabilistic Latent Space of Object Shapes via 3D Generative-Adversarial Modeling](https://mlsanity.com/paper/1610.07584/) (2016)
- [DISN: Deep Implicit Surface Network for High-quality Single-view 3D Reconstruction](https://mlsanity.com/paper/1905.10711/) (2019)
- [Learning to Predict 3D Objects with an Interpolation-based Differentiable Renderer](https://mlsanity.com/paper/1908.01210/) (2019)
- [PQ-NET: A Generative Part Seq2Seq Network for 3D Shapes](https://mlsanity.com/paper/1911.10949/) (2019)
- [Deep Level Sets: Implicit Surface Representations for 3D Shape Inference](https://mlsanity.com/paper/1901.06802/) (2019)
- [Autoregressive 3D Shape Generation via Canonical Mapping](https://mlsanity.com/paper/2204.01955/) (2022)
- [Pixels, voxels, and views: A study of shape representations for single view 3D object shape prediction](https://mlsanity.com/paper/1804.06032/) (2018)
- [Deep Implicit Statistical Shape Models for 3D Medical Image Delineation](https://mlsanity.com/paper/2104.02847/) (2021)
- [SP-GAN: Sphere-Guided 3D Shape Generation and Manipulation](https://mlsanity.com/paper/2108.04476/) (2021)

## Abstract (arXiv)

Fluorescence microscopy is a quintessential tool for observing cells and understanding the underlying mechanisms of life-sustaining processes of all living organisms. The problem of extracting 3D shape of mitochondria from fluorescence microscopy images remains unsolved due to the complex and varied shapes expressed by mitochondria and the poor resolving capacity of these microscopes. We propose an approach to bridge this gap by learning a shape prior for mitochondria termed as MiShape, by leveraging high-resolution electron microscopy data. MiShape is a generative model learned using implicit representations of mitochondrial shapes. It provides a shape distribution that can be used to generate infinite realistic mitochondrial shapes. We demonstrate the representation power of MiShape and its utility for 3D shape reconstruction given a single 2D fluorescence image or a small 3D stack of 2D slices. We also showcase applications of our method by deriving simulated fluorescence microscope datasets that have realistic 3D ground truths for the problem of 2D segmentation and microscope-to-microscope transformation.