CellProfiler 4: improvements in speed, utility and usability
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Summary
CellProfiler 4 provides significantly improved performance in complex workflows compared to previous versions, and has made several user interface refinements to improve the usability of the software.
- Type
- article
- Published
- 2021-06-30
- Cited by
- 1,784
- References
- 20
- Access
- Open access
- OpenAlex
- https://openalex.org/W3196897371
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:235718146
Keywords
Computer science, Usability, Workflow, Software, Modular design
References
- NIH Image to ImageJ: 25 years of Image Analysis
- Annotated high-throughput microscopy image sets for validation
- CellProfiler: image analysis software for identifying and quantifying cell phenotypes
- Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software
- Adaptive document image binarization
- Review of free software tools for image analysis of fluorescence cell micrographs
- Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes
- Dask: Parallel Computation with Blocked algorithms and Task Scheduling
- QuPath: Open source software for digital pathology image analysis
- CellProfiler 3.0: Next-generation image processing for biology
- ilastik: interactive machine learning for (bio)image analysis
- Cellpose: a generalist algorithm for cellular segmentation
- nucleAIzer: A Parameter-free Deep Learning Framework for Nucleus Segmentation Using Image Style Transfer
- Using Jupyter for Reproducible Scientific Workflows
- Cell Detection with Star-convex Polygons
- scikit-image: image processing in Python
- Distributed under Creative Commons Cc-by 4.0 Scikit-image: Image Processing in Python
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- 2020 BioImage Analysis Survey: Community experiences and needs for the future
- Cell Painting predicts impact of lung cancer variants
- Morphological profiling of environmental chemicals enables efficient and untargeted exploration of combination effects
- A User-Friendly Approach for Routine Histopathological and Morphometric Analysis of Skeletal Muscle Using CellProfiler Software
- Functional, metabolic and transcriptional maturation of human pancreatic islets derived from stem cells
- Pituitary Gonadotropin Gene Expression During Induced Onset of Postsmolt Maturation in Male Atlantic Salmon: In Vivo and Tissue Culture Studies
- MultiHeadGAN: A Deep Learning Method for Low Contrast Retinal Pigment Epithelium Cells Segmentation in Fluorescent Flatmount Microscopy Images
- Multiplexed microfluidic chip for cell co-culture
- Hypothalamic-pituitary-adrenal axis dysfunction worsens epilepsy outcomes and increases SUDEP risk
- Adjusting the neuron to astrocyte ratio with cytostatics in hippocampal cell cultures from postnatal rats: A comparison of cytarabino furanoside (AraC) and 5-fluoro-2’-deoxyuridine (FUdR)
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- High-throughput Oligopaint screen identifies druggable regulators of genome folding
- Obscurin regulates ankyrin macromolecular complex formation.
- Molecular differences in APOBEC3 counteraction by primate herpesviruses reveal an evolutionary link between the genesis of APOBEC3B and novel viral ribonucleotide reductase function
- Centriolar satellites expedite mother centriole remodeling to promote ciliogenesis
- p97/UBXD1 Generate Ubiquitylated Proteins That Are Sequestered into Nuclear Envelope Herniations in Torsin-Deficient Cells
- Fluorescence complementation enables quantitative imaging of cell penetrating peptide-mediated protein delivery in plants including WUSCHEL transcription factor
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