Robert Cudmore

Image Analysis

Map Manager Full featured, accurate, and intuitive software to mark spines and manage connections between multiple imaging sessions.
Map Tracker Version 1 documentation is still available here
Vascular Analysis
An Igor Pro program to trace and analyze 3D volumes of vasculature.

Data Acquisition

mp285 Canvas An Igor Pro program that integrates with ScanImage to allow the creation of an intuitive canvas to visually and spatially browse 3d images. This is used for both in vivo and ex vivo experiments.
Treadmill A collection of software to control an experiment with an Arduino using an intuitive web interface. In particular, this version will control a treadmill that is used during an awake in vivo experiment.
bAcq/bStim A program that performs stimulus generation and data acquisition. Written in Igor Pro and works with National Instruments boards.
bMovie bMovie is a general purpose video and image acquisition program that runs in Igor Pro.

Image Analysis Macros

bAlignBatch Batch process a directory of .tif (or .lsm) files, applying median filter and stack alignment. bAlignBatch is a ImageJ/Fiji macro and utilizes the MultiStackReg plugin.
Bob Neurite Tracer A derivation of the ImageJ/Fiji plugin Simple Neurite Tracer that will find dendritic/axonal backbones using a text file specifying a sparse set of 3D control points. Can be run in batch mode to find dendrites across a large number of 3D image stacks. Used by Map Tracker.
Sliding Z-Projection Takes an input stack and creates a new stack which is the sliding Z-Projection of the input. A sliding Z-Projection is a stack where each image slice is a Z-Projection (+/- a number of slices) of the input.


For a description of my electrophysiology software, go here.
Dept. of Neuroscience, Linden Lab Johns Hopkins Medicine © 2008-2012