BaSiCPy: Scalable and Robust Shading Correction for Optical Microscopy Images

bioRxiv · 27 Oct 2026 · Preprint · Open access

Liu, Fukai + 19 more

The abstract is read at the publisher; the summary is JClub's.

BaSiCPy, a foreground-aware BaSiC implementation for optical fluorescence microscopy, improves illumination profile estimation under strongly correlated foreground structures and adds automatic hyperparameter selection.

Why it matters: Illumination variation and temporal intensity drift can confound quantitative fluorescence microscopy, and BaSiC can fail when foreground content is strongly correlated across images.
What they did: BaSiCPy uses a foreground-aware approach to estimate illumination profiles, selects hyperparameters automatically, and accelerates large-scale processing with GPU support.
The result: The open-source Python package includes graphical and programmatic interfaces, enabling more reproducible, scalable integration into bioimage analysis workflows.

Open access

FlyAnatoView: Visualization of Drosophila Single-cell RNA-seq Datasets on Anatomographs
bioRxiv · 27 Oct 2026 · Preprint
FlyAnatoView projects Drosophila melanogaster single-cell RNA-seq gene expression onto anatomical diagrams to restore spatial context lost during tissue dissociation.
- Open access
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https://jclub.com.au/a/10.64898/2026.09.28.755010
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scTGCL: A Transformer-Based Graph Contrastive Learning Approach for Efficiently Clustering Single-Cell RNA-seq Data
bioRxiv · 26 Oct 2026 · Preprint
scTGCL, a Transformer-based graph contrastive learning method for scRNA-seq, achieves the highest average clustering performance across twenty real and simulated datasets, improving accuracy, NMI, and ARI.
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https://jclub.com.au/a/10.64898/2026.03.28.714542
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Cortex-Wide, Cellular-Resolution Volumetric Imaging with a Modular Two-Photon Imaging Platform
bioRxiv · 24 Oct 2026 · Preprint
Meso2P sustains an effective NA 0.87 over a contiguous 6 * 6 mm^2 FOV at 7.67 Hz (2,048 * 2,048 pixels), enabling cortex-wide single-cell imaging.
- Open access
- 2 cites
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https://jclub.com.au/a/10.1101/2025.07.03.662899
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BaSiCPy: Scalable and Robust Shading Correction for Optical Microscopy Images

Related in JClub

FlyAnatoView: Visualization of Drosophila Single-cell RNA-seq Datasets on Anatomographs

scTGCL: A Transformer-Based Graph Contrastive Learning Approach for Efficiently Clustering Single-Cell RNA-seq Data

Cortex-Wide, Cellular-Resolution Volumetric Imaging with a Modular Two-Photon Imaging Platform

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