dNEMO

dNEMO quantifies fluorescent puncta in single-cell microscopy images to measure diffraction-limited molecular assemblies such as smFISH transcripts and IKK/NEMO puncta dynamics.

Key Features:

• Spot Detection (à trous wavelet transform): Uses the à trous wavelet transform for computationally efficient detection of diffraction-limited spots with robustness to imaging noise in fixed-cell and time-lapse images.
• Segmentation: Performs segmentation to assign detected puncta to single cells for per-cell quantification.
• Local Background Measurement: Measures puncta intensity against local background to extract quantitative single-cell data.
• Application Examples: Applied to single-molecule fluorescence in situ hybridization (smFISH) for transcript counting and to time-lapse analysis of transient IKK/NEMO puncta formed in cells exposed to inflammatory stimuli.

Scientific Applications:

• smFISH quantification: Counting individual transcripts in single cells using single-molecule FISH data.
• Signal transduction dynamics: Analyzing formation and dynamics of IKK/NEMO puncta in response to inflammatory stimuli.
• Molecular assembly studies: Quantifying dynamic molecular assemblies to study gene expression and signal transduction in cell biology, genomics, and immunology.

Methodology:

Applies the à trous wavelet transform for noise reduction and spot detection, followed by segmentation and local background measurement to quantify fluorescent puncta in fixed-cell and time-lapse single-cell images.