SuperSegger/OmniSegger is a completely automated MATLAB-based trainable image cell segmentation, fluorescence quantification and analysis suite, particularly well suited for high-throughput time-lapse fluorescence microscopy of in vivo bacterial cells.

NEW! SuperSegger has also been modified to work with the improved segmentation of Omnipose. OmniSegger can be found here.

The original SuperSegger website can be found here, with the Github here.

Omnipose solves the over-segmentation problems of Cellpose, a generalist algorithm for cell and nucleus segmentation, for large, anisotropic cells. This is particularly relevant for bacterial cells, but Omnipose is suitable for arbitrary cell shapes. Click here to download.

Curve Filter is a matlab-based tool for finding punctate foci in fluorescent microscopy images.

Click here to download.

Steppi is a matlab-based tool for change-point analysis. We present a unified approach to the analysis of processes whose noise can be modeled by Gaussian, Wiener or Ornstein-Uhlenbeck Processes. We expect this technique to be of general interest to experimental investigators interested in biological systems. Applications of this analysis include molecular-motor stepping, fluorophore bleaching, electrophysiology, particle and cell tracking, detection of copy number variation by sequencing, tethered- particle-motion etc.

Click here for information and download.

Trace is a matlab-based polymer tracking software package which we have used for tracing DNA contours. Click here to download.