Pincus Lab

Washington University School of Medicine

Department of Developmental Biology
and Department of Genetics

For the latest, check out our github repositories.

Celltool

Celltool is a collection of tools for analysis of shapes from images, and in particular, for analyzing cell shapes from micrographs. Celltool provides methods for extracting shapes from images, aligning and measuring those shapes, plotting shapes, and statistically comparing distributions (usually of shape measurements). Celltool is open-source (GPL); more information including software downloads and a tutorial can be found on the main Celltool page.

To refer to Celltool in a publication, please cite:

Pincus Z & Theriot JA. Comparison of quantitative methods for cell-shape analysis. J Microscopy 227 pp. 140–156 (2007).

IOTool

IOTool is firmware for AVR microcontrollers (Arduinos and similar) that enables basic GPIO functions (pin outputs off, on, and PWM; digital and analog input; and timing and looping functions) to be controlled from a host computer over a simple serial interface. This is useful for interfacing a computer with various hardware devices with TTL controls (common in microscopy), and allowing for high-precision sequencing of those devices.

freeimage-py

freeimage-py is our basic image IO library for the lab. It provides a simple interface for reading and writing image files to/from numpy arrays in python.

ISMBuffer

ISMBuffer provides a simple way to share memory between arbitrary python processes. We use it to enable zero-copy transfers of large image data from one process to another.

zplib

zplib is a collection of general-purpose utility functions for image analysis, simple statistics, and curve geometry. This code is both used in the Pincus lab and serves as a good tutorial for how to use the scipy modules which underlie many of these routines.

zbar-py

zbar-py is a simple python interface for reading barcodes (including QR codes) from numpy arrays. This interface is a thin wrapper around the zbar barcode reading package.