WideField

This module provides tools for processing widefield video sequence data.

Sequence Preprocessing

A preprocessing pipeline for widefield calcium imaging data. Computes ΔF/F with time-varying baseline using rolling window percentile calculation.

Features:

  • Motion correction using ECC (Enhanced Correlation Coefficient) algorithm

  • Rolling window baseline (F0) calculation with configurable percentile

  • ΔF/F computation with interpolated baseline

  • GPU acceleration support (CuPy) and Numba JIT optimization

  • Memory-efficient chunked processing for large datasets

CLI Usage:

$ nl_wfield preproc --file <TIF_FILE> [OPTIONS]
$ nl_wfield preproc --directory <TIF_DIR> [OPTIONS]

Options:

Data I/O Options:
  --file FILE           Single input TIF file
  --directory DIR       Directory containing TIF files
  --suffix SUFFIX       File suffix pattern (default: .tif)
  --output_dir DIR      Output directory for results

Processing Options:
  --motion_corr         Enable motion correction
  --max_shift N         Max shift in pixels for motion correction (default: 20)
  --rotate DEGREES      Rotate all sequences by specified degrees
  --chunk_size N        Frames per processing chunk (default: 3000)
  --window_size N       Rolling baseline window size in frames (default: 100)
  --percentile N        Percentile for baseline calculation (default: 10)
  --n_jobs N            Parallel jobs (-1 = all CPUs, default: -1)
  --force_compute       Force recomputation even if outputs exist
  --save_f0             Save F0 baseline to disk

Acceleration Options:
  --use_gpu             Use GPU acceleration with CuPy

Example:

# Basic preprocessing
$ nl_wfield preproc --file recording.tif

# With motion correction and GPU acceleration
$ nl_wfield preproc --directory ./tifs --motion_corr --use_gpu

# Custom parameters
$ nl_wfield preproc --file data.tif --window_size 200 --percentile 5 --rotate 90

Output Files:

  • dff.npy: ΔF/F array (T, H, W)

  • f0.h5: F0 baseline array (if --save_f0 enabled)

  • reference_frame.tif: Mean reference frame

  • motion_transforms.h5: Motion correction transforms (if --motion_corr enabled)

  • metadata.json: Processing parameters and data info

API reference:

Widefield Transform

The transform GUI registers widefield images to a dorsal cortex map. It supports interactive point-pair selection, projective or similarity transforms, RANSAC outlier handling, transform export, and live transformed-frame overlays.

CLI Usage:

$ nl_wfield trans

API reference:

FFT View with Bokeh

A Bokeh-based visualization of the HSV colormap representation of the Fourier-transformed video (e.g., for visual retinotopy).

Usage:

nl_wfield fft <FILE>

fft_view

Align with Napari

A Napari-based tool for aligning video data to a dorsal cortex view.

Usage:

nl_wfield align <FILE> [-R REFERENCE_FILE] [-M MAP_FILE]

align_view