ArticlePloS one2020
FalseColor-Python: A rapid intensity-leveling and digital-staining package for fluorescence-based slide-free digital pathology.
Article in PloS one, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- 3D multi-omics tumour atlases: from technology to biology and clinical translation.Nature reviews. Cancer · 2026Review
- Deep-learning triage of three-dimensional pathology datasets for comprehensive and efficient pathologist assessments.Nature biomedical engineering · 2026Article
- Assessing the Effects of a 3-Dimensional (3D) Pathology Tissue-Processing Workflow on Downstream Molecular Analyses.Laboratory investigation; a journal of technical methods and pathology · 2026Article
- Prototype-based AI triage for 3D pathology.bioRxiv : the preprint server for biology · 2026Article
- 3D pathology-guided microdissection.Nature methods · 2026Article
- Hybrid solid-liquid optics enable scalable, high-resolution light-sheet microscopy across diverse immersion media.Nature biotechnology · 2026Article
- Volumetric Cyclic Immunofluorescence for 3D Spatial Profiling of Immune Structures in Human FFPE Tissue.bioRxiv : the preprint server for biology · 2026Article
- Assessing the effects of a 3D pathology tissue-processing workflow on downstream molecular analyses.bioRxiv : the preprint server for biology · 2026Article
- Prediction of outcome from spatial Protein profiling of triple-negative breast cancers.Communications medicine · 2026Article
- 3D pathology-guided microdissection.bioRxiv : the preprint server for biology · 2025Article
- Hybrid Solid-Liquid Optics Enable Scalable, High-Resolution, Multi-Immersion Light-Sheet Microscopy.bioRxiv : the preprint server for biology · 2025Article
- First application of three-dimensional light sheet fluorescence microscopy to human testicular tumors: New perspectives in histopathology.Andrology · 2025Article
- Vaginal biomechanical function in premenopausal and postmenopausal women with and without pelvic organ prolapse.Scientific reports · 2025Article
- Investigating hepatic fibrosis heterogeneity by three-dimensional imaging in metabolic dysfunction-associated steatotic liver disease.Scientific reports · 2025Article
- Basic Uses of Python for Research in Our Laboratory: Examples of Data Analysis, and Processing of Histological Samples Based on the Special Graduate Lecture for Postgraduate Students Presented on January 2025.Juntendo medical journal · 2025Review
- Exploring Multiplex Immunohistochemistry (mIHC) Techniques and Histopathology Image Analysis: Current Practice and Potential for Clinical Incorporation.Cancer medicine · 2025Review
- Axially swept open-top light-sheet microscopy for densely labeled clinical specimens.Optics letters · 2024Article
- descSPIM: an affordable and easy-to-build light-sheet microscope optimized for tissue clearing techniques.Nature communications · 2024Article
- Article
- An end-to-end workflow for nondestructive 3D pathology.Nature protocols · 2024Review
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4 authors.
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Abstract
Slide-free digital pathology techniques, including nondestructive 3D microscopy, are gaining interest as alternatives to traditional slide-based histology. In order to facilitate clinical adoption of these fluorescence-based techniques, software methods have been developed to convert grayscale fluorescence images into color images that mimic the appearance of standard absorptive chromogens such as hematoxylin and eosin (H&E). However, these false-coloring algorithms often require manual and iterative adjustment of parameters, with results that can be inconsistent in the presence of intensity nonuniformities within an image and/or between specimens (intra- and inter-specimen variability). Here, we present an open-source (Python-based) rapid intensity-leveling and digital-staining package that is specifically designed to render two-channel fluorescence images (i.e. a fluorescent analog of H&E) to the traditional H&E color space for 2D and 3D microscopy datasets. However, this method can be easily tailored for other false-coloring needs. Our package offers (1) automated and uniform false coloring in spite of uneven staining within a large thick specimen, (2) consistent color-space representations that are robust to variations in staining and imaging conditions between different specimens, and (3) GPU-accelerated data processing to allow these methods to scale to large datasets. We demonstrate this platform by generating H&E-like images from cleared tissues that are fluorescently imaged in 3D with open-top light-sheet (OTLS) microscopy, and quantitatively characterizing the results in comparison to traditional slide-based H&E histology.
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