Instytut Podstawowych Problemów Techniki
Polskiej Akademii Nauk

Partnerzy

T. Shimogori


Prace konferencyjne
1.  Poon Ch., Rachmadi M.F., Byra M., Schlachter M., Xu B., Shimogori T., Skibbe H., AN AUTOMATED PIPELINE TO CREATE AN ATLAS OF IN SITU HYBRIDIZATION GENE EXPRESSION DATA IN THE ADULT MARMOSET BRAIN, ISBI, 2023 IEEE 20th International Symposium on Biomedical Imaging, 2023-04-18/04-21, Cartagena (CO), DOI: 10.1109/ISBI53787.2023.10230544, pp.1-5, 2023

Streszczenie:
We present the first automated pipeline to create an atlas of in situ hybridization gene expression in the adult marmoset brain in the same stereotaxic space. The pipeline consists of segmentation of gene expression from microscopy images and registration of images to a standard space. Automation of this pipeline is necessary to analyze the large volume of data in the genome-wide whole-brain dataset, and to process images that have varying intensity profiles and expression patterns with minimal human bias. To reduce the number of labelled images required for training, we develop a semi-supervised segmentation model. We further develop an iterative algorithm to register images to a standard space, enabling comparative analysis between genes and concurrent visualization with other datasets, thereby facilitating a more holistic understanding of primate brain structure and function.

Słowa kluczowe:
contrastive learning, gene atlas, segmen-tation, semi-supervised learning, registration

Afiliacje autorów:
Poon Ch. - inna afiliacja
Rachmadi M.F. - inna afiliacja
Byra M. - IPPT PAN
Schlachter M. - inna afiliacja
Xu B. - Tsinghua University (CN)
Shimogori T. - inna afiliacja
Skibbe H. - inna afiliacja
2.  Byra M., Poon Ch., Shimogori T., Skibbe H., Implicit Neural Representations for Joint Decomposition and Registration of Gene Expression Images in the Marmoset Brain, MICCAI 2023, Medical Image Computing and Computer-Assisted Intervention, 2023-10-08/10-12, Vancouver (CA), DOI: 10.48550/arXiv.2308.04039, pp.1, 2023

Streszczenie:
We propose a novel image registration method based on implicit neural representations that addresses the challenging problem of registering a pair of brain images with similar anatomical structures, but where one image contains additional features or artifacts that are not present in the other image. To demonstrate its effectiveness, we use 2D microscopy in situ hybridization gene expression images of the marmoset brain. Accurately quantifying gene expression requires image registration to a brain template, which is difficult due to the diversity of patterns causing variations in visible anatomical brain structures. Our approach uses implicit networks in combination with an image exclusion loss to jointly perform the registration and decompose the image into a support and residual image. The support image aligns well with the template, while the residual image captures individual image characteristics that diverge from the template. In experiments, our method provided excellent results and outperformed other registration techniques.

Słowa kluczowe:
brain, deep learning, gene expression, implicit neural representations, registration

Afiliacje autorów:
Byra M. - IPPT PAN
Poon Ch. - inna afiliacja
Shimogori T. - inna afiliacja
Skibbe H. - inna afiliacja
140p.

Abstrakty konferencyjne
1.  Poon Ch., Rachmadi M.F., Byra M., Shimogori T., Skibbe H., Semi-supervised contrastive learning for semantic segmentation of ISH gene expression in the marmoset brain, NEURO2022, The 45th Annual Meeting of the Japan Neuroscience Society The 65th Annual Meeting of the Japanese Society for Neurochemistry The 32nd Annual Conference of the Japanese Neural Network Society, 2022-06-30/07-03, Okinawa (JP), pp.1, 2022

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