GLOM•MAP
GLOM•MAP is a toolbox written for the MATLAB development enviroment, which can be obtained for a reasonable student license. Since GLOM•MAP was written for MATLAB, it works equally as well on the PC as on the MAC. GLOM•MAP consists of two components: 1. OBS can be used to map the location of glomeruli in transverse sections of the olfactory bulb. 2. GDB can be used to transform the OBS data and to analyze the collected glomerular activity data. This data can be scored and mapped in the radial and anterio-posterior dimensions as discussed in Salcedo et al, 2005.
Installation. After downloading the files, unzip each file and move the GDBHome and OBSHome folder to the MATLAB work directory. You then need to add the directory paths of these folders to the MATLAB file path (see the User Guide for more detailed instrucutions). Follow the same procedure to install the gProcess plugin. To install the gBrowser plugin, simply add the .m and .fig files to the GDBHome plugins folder.
To launch, type 'gdb' or 'obs' in the MATLAB command window.
When upgrading, make sure to quit OBS and GDB first and then drag the new gdbhome or obshome into the work folder and completely overwrite the old folders. Old mapping projects may need to be upgraded to the latest file format after upgrading. Simply click on the File Conversion button in OBS and select the slice_data.mat file.
We have also made available two sample mapping projects for OBS that employ either the L Plane or the Leon/Johnson mapping technique. In these projects, we have mapped several instructive sections according to the appropriate mapping technique. You can save the unzipped directories anwhere you like. After downloading and unzipping, launch OBS and browse to the images directory. Open any image (or the slice_data.mat) file to launch. For more information, please contact ernesto.salcedo@uchsc.edu.
Download the latest versions of our Software Here:
| NAME | version | description | update | link |
| GDB | 1.1.26 | GLOM•MAP module for data analysis | 2/28/2007 | GdbHome.zip |
| OBS | 1.1.34a | GLOM•MAP module for mapping bulbs | 08/25/2007 | obshome.zip |
| gProcess | GDB plugin - collates mapped glomerular cross-sections | 1/28/2007 | gProcess.zip | |
| gBrowser | GDB plugin - generates statistics on cross-sections or collated glomeruli | 4/23/2006 | gBrowser.zip | |
| User Guide | 1/16/2008 | GLOM-MAP manual.pdf | ||
| Sample L Plane | Sample mapping project for OBS using our mapping technique | Sample Images.zip | ||
| Sample Leon/Johnson | Sample mapping project for OBS using the Leon/Johnson mapping technique | Sample LJ Images.zip |
Other Useful Matlab software
| Name | Function | updated |
| RGB_merge | merges 3 (or 2) gray scale images into a single RGB image. Useful for large scale imaging projects where many grayscale images need to be merged in RGB images. | 2/6/2007 |
Glomerular Analysis 2.0
Glomerular_Analysis is a plugin for ImageJ that allows the user to determine glomerular location in transverse sections of the olfactory bulb. Download the Glomerular_Analysis.zip file and unzip in the plugins directory of ImageJ. Then follow instructions in Glomerular_Analysis.rtf.
Download Glomerular Analysis Plugin for Mac OS X Here.
MLPEST
The following programs are written in C for use with the olfactometer of Bodyak and Slotnick. Begin.exe is the equivalent of BeginD in Qbasic--it is the first program used to train a mouse for the olfactometer. Begin.exe trains the animal to lick at the water delivery port to receive a water reward. Splus_minus.exe is the equivalent of S+S- in Qbasic; it is used to train the animal to lick when an odor stimulus is present and refrain from licking when no odor stimulus is present. Splus_minus.exe can also be used for determining the number of blocks required to reach criterion on a simple detection task. MLPestThreshold has no equivalent in Qbasic. It uses MLPEST methodology to determine odorant detection threshold.
Two simulation programs are also included and do not require an olfactometer. MLPestTresholdSim.exe is identical to MLPestThreshold except that a simulated mouse is run through the program. Users specify simulation parameters. MLPestSim.exe is similar to MLPestThresholdSim.exe except that it runs 500 simulated mice through the program and outputs the results for all 500 runs.
Download MLPEST here.