Analysis workflow notebooks¶

Compression metric calculations¶

Metrics for comparing traces of compressed fibers¶

Analysis combines compression simulations from Cytosim and Readdy and calculates various compression metrics to compare fibers.

Compare compression metrics between simulators (source | notebook)

Dimensionality reduction¶

Single actin fiber compressed at different compression velocities¶

Analysis combines compression simulations from Cytosim and Readdy and applies dimensionality reduction to individual fibers aligned in the yz-plane to the positive y axis, keeping x axis coordinates unchanged.

Run PCA on compression simulations (source | notebook)
Run PaCMAP on compression simulations (source | notebook)

Tomography data¶

Actin CME tomography data¶

Load, process, and analyze segmented cryo-electron tomography data of CME-associated actin filaments.

Analyze tomography data (source | notebook)

Wall clock times¶

Single actin fiber compressed at different compression velocities¶

Analysis extracts wall clock times from the ACTIN_COMPRESSION_VELOCITY simulation series, which simulates compression of a single 500 nm actin fiber at four different velocities (4.7, 15, 47, and 150 μm/s) with five replicates.

Summarize Cytosim compression simulation wall clock times (source | notebook)