Microscopy preprints – bioimage analysis

Posted by FocalPlane, on 3 May 2024

Here is a curated selection of preprints published recently. In this post, we focus specifically on bioimage analysis.

FInCH: FIJI plugin for automated and scalable whole-image analysis of protein expression and cell morphology
Cody A. Lee, Carmen Sánchez Moreno, Alexander V. Badyaev

Gossamer: Scaling Image Processing and Reconstruction to Whole Brains
Karl Marrett, Keivan Moradi, Chris Sin Park, Ming Yan, Chris Choi, Muye Zhu, Masood Akram, Sumit Nanda, Qing Xue, Hyun-Seung Mun, Adriana Gutierez, Mitchell Rudd, Brian Zingg, Gabrielle Magat, Kathleen Wijaya, Hongwei Dong, X. William Yang, Jason Cong

Figure extracted from Marrett, *et al..* The image is made available under a CC-BY 4.0 International license.

A Quantitative Metric of Confidence For Segmentation of Nuclei in Large Spatially Variable Image Volumes
Liming Wu, Alain Chen, Paul Salama, Kenneth W. Dunn, Seth Winfree, Edward J. Delp

Figure extracted from Wu, *et al..* The image is made available under a CC-BY-NC 4.0 International license.

StomaVision: stomatal trait analysis through deep learning
Ting-Li Wu, Po-Yu Chen, Xiaofei Du, Heiru Wu, Jheng-Yang Ou, Po-Xing Zheng, Yu-Lin Wu, Ruei-Shiuan Wang, Te-Chang Hsu, Chen-Yu Lin, Wei-Yang Lin, Ping-Lin Chang, Chin-Min Kimmy Ho, Yao-Cheng Lin

SPACe (Swift Phenotypic Analysis of Cells): an open-source, single cell analysis of Cell Painting data
Fabio Stossi, Pankaj K. Singh, Michela Marini, Kazem Safari, Adam T. Szafran, Alejandra Rivera Tostado, Christopher D. Candler, Maureen G. Mancini, Elina A. Mosa, Michael J. Bolt, Demetrio Labate, Michael A. Mancini

Analysis Pipeline to Quantify Uterine Gland Structural Variations
Sameed Khan, Adam Alessio, Ripla Arora

STARDUST: a pipeline for the unbiased analysis of astrocyte regional calcium dynamics
Yifan Wu, Yanchao Dai, Katheryn B. Lefton, Timothy E. Holy, Thomas Papouin

Figure extracted from Wu, *et al..* The image is made available under a CC-BY 4.0 International license.

da_Tracker: Automated workflow for high throughput single cell and single phagosome tracking in infected cells
Jacques Augenstreich, Anushka Poddar, Ashton T. Belew, Najib M El-Sayed, Volker Briken

SynBot: An open-source image analysis software for automated quantification of synapses
Justin T. Savage, Juan Ramirez, W. Christopher Risher, Yizhi Wang, Dolores Irala, Cagla Eroglu

SwinCell: a transformer-based framework for dense 3D cellular segmentation
Xiao Zhang, Zihan Lin, Liguo Wang, Yong S. Chu, Yang Yang, Xianghui Xiao, Yuewei Lin, Qun Liu

Figure extracted from Zhang, *et al*. The image is made available under a CC-BY-NC 4.0 International license.

OrgaMeas: A pipeline that integrates all the processes of organelle image analysis
Taiki Baba, Akimi Inoue, Susumu Tanimura, Kohsuke Takeda

Self-supervised Vision Transformers for image-to-image labeling: a BiaPy solution to the LightMyCells Challenge
Daniel Franco-Barranco, Aitor González-Marfil, Ignacio Arganda-Carreras

Figure extracted from Franco-Barranco, *et al.* The image is made available under a CC-BY 4.0 International license.

VISION — an open-source software for automated multi-dimensional image analysis of cellular biophysics
Florian Weber, Sofiia Iskrak, Franziska Ragaller, Jan Schlegel, Birgit Plochberger, Erdinc Sezgin, Luca A. Andronico

ViM-UNet: Vision Mamba for Biomedical Segmentation
Anwai Archit, Constantin Pape

Deep learning-driven imaging of cell division and cell growth across an entire eukaryotic life cycle
Shreya Ramakanth, Taylor Kennedy, Berk Yalcinkaya, Sandhya Neupane, Nika Tadic, Nicolas E. Buchler, Orlando Argüello-Miranda

An image processing pipeline for electron cryo-tomography in RELION-5
Alister Burt, Bogdan Toader, Rangana Warshamanage, Andriko von Kügelgen, Euan Pyle, Jasenko Zivanov, Dari Kimanius, Tanmay A.M. Bharat, Sjors H.W. Scheres