EfficientCellSeg: Efficient Volumetric Cell Segmentation Using Context Aware Pseudocoloring

Royden Wagner, Karl Rohr

Keywords: Volumetric cell segmentation, deep learning, pseudocoloring, context awareness, parameter efficiency

Abstract: Volumetric cell segmentation in fluorescence microscopy images is important to study a wide variety of cellular processes. Applications range from the analysis of cancer cells to behavioral studies of cells in the embryonic stage. Like in other computer vision fields, most recent methods use either large convolutional neural networks (CNNs) or vision transformer models (ViTs). Since the number of available 3D microscopy images is typically limited in applications, we take a different approach and introduce a small CNN for volumetric cell segmentation. Compared to previous CNN models for cell segmentation, our model is efficient and has an asymmetric encoder-decoder structure with very few parameters in the decoder. Training efficiency is further improved via transfer learning. In addition, we introduce Context Aware Pseudocoloring to exploit spatial context in z-direction of 3D images while performing volumetric cell segmentation slice-wise. We evaluated our method using different 3D datasets from the Cell Segmentation Benchmark of the Cell Tracking Challenge. Our segmentation method achieves top-ranking results, while our CNN model has an up to 25x lower number of parameters than other top-ranking methods. Code and pretrained models are available at: https://github.com/roydenwa/efficient-cell-seg

Registration: I acknowledge that publication of this at MIDL and in the proceedings requires at least one of the authors to register and present the work during the conference.

Authorship: I confirm that I am the author of this work and that it has not been submitted to another publication before.

Paper Type: validation/application paper

Primary Subject Area: Segmentation

Secondary Subject Area: Transfer Learning and Domain Adaptation

Confidentiality And Author Instructions: I read the call for papers and author instructions. I acknowledge that exceeding the page limit and/or altering the latex template can result in desk rejection.

Code And Data: https://github.com/roydenwa/efficient-cell-seg

Community Implementations: [ 2 code implementations](https://www.catalyzex.com/paper/efficientcellseg-efficient-volumetric-cell/code)