Neuroscience Software Download:

These are the tools and applications developed during the course of my studies.

Please email if you have any comments or issues.

Simulation Tools

FM-Sim - Fluorescence Microscopy Simulation - current version 0.4 (22-07-2014)

This Java application allows the definition of fluorescence microscopy experimental protocols to study CNS synaptic terminals. These defined protocols may be simulated, and given adequated observed experimental data, rate parameters for the simulation model may be automatically inferred.

Runnable Java archive

User Guide
[In Progress]

Project source (as Eclipse project archive)
Available on request

Image Processing Tools

The following are tools developed to make FM image processing and analysis a little easier.

ROI Trace Selection - current version 0.21 (02-08-2022)

A web based rewrite of the Java tool below.

User Guide

Project source

ROI Trace Selection - current version 0.11 (15-12-2015)

This Java tool is designed to assist in selection of Regions of Interest (ROIs) which conform to expected behaviour. It should make the ROI selection data preprocessing stage of ROI analysis slightly less painful. The tool provides a simple graph visualisation of a full set of ROI timecourse traces. The user may then select or deselect individual traces, scale and offset the traces, and then output the results in CSV format.

Additionally, as ROIs tend to follow an expected pattern for a given dataset, ROIs which do not follow this behaviour can be automatically excluded. These patterns are specified as percentage drops or increases in fluorescence within a given frame interval, the percentage being of the total fluorescence drop or increase. For example, select those ROIs which exhibit a 20% drop in fluorescence between frames 18 and 20, which corresponds with the time a large stimulus was applied during the assay.

Runnable Java archive

User Guide

Project source (as Eclipse project archive)
Available on request


Unless otherwise stated, these projects are licenced under the GNU Lesser General Public Licence Version 3 (LGPLv3). Included third party libraries are released under their respective licences, listed below. This is an aggregate of all libraries used in all Image Processing Tools projects.

Library Home site License
ImageJ v1.46 Public domain -
commons io v2.4
commons math v3.3.2
log4j v1.2.15
slf4j v1.5.10
jcommon v1.0.21
jfreechart v1.0.17
LOCI Bioformats ImageJ plugin libraries v4.4.6
JGoodies Forms v1.3
opencsv v2.3
TableLayout v2009-08-26 Open source (custom) licence in source code


This work was supported in part by grants EP/F500385/1 and BB/F529254/1 for the University of Edinburgh School of Informatics Doctoral Training Centre in Neuroinformatics and Computational Neuroscience ( from the UK Engineering and Physical Sciences Research Council (EPSRC), UK Biotechnology and Biological Sciences Research Council (BBSRC), and the UK Medical Research Council (MRC). The work has made use of resources provided by the Edinburgh Compute and Data Facility (ECDF;, which has support from the eDIKT initiative (


This software is provided by the copyright holders and contributors "as is" and any express or implied warranties, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose are disclaimed. In no event shall the copyright holder or contributors be liable for any direct, indirect, incidental, special, exemplary, or consequential damages (including, but not limited to, procurement of substitute goods or services; loss of use, data, or profits; or business interruption) however caused and on any theory of liability, whether in contract, strict liability, or tort (including negligence or otherwise) arising in any way out of the use of this software, even if advised of the possibility of such damage.