Robert Cudmore

Image Analysis

Map Manager Full featured, accurate, and intuitive software to annotate 3D image time-series.
Vascular Analysis
Software to trace and analyze vascular networks in 3D image time-series.

Data Acquisition

Treadmill A complete hardware/software solution to build an 'on the scope' motorized treadmill with synchronized video to be used during awake in vivo two-photon imaging.
Canvas Software to create an intuitive spatial 'canvas' that is used during both in vivo and ex vivo imaging as well as offline during analysis.
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