National Resource for Imaging Mass Spectrometry ================================== PRODUCT DESCRIPTION ================================== OpenMIMS version 2.5 (June 2012) OpenMIMS is an ImageJ plugin designed to open, process and analyze images captured with NanoSIMS 50 & 50L secondary ion mass spectrometers (Cameca). The OpenMIMS plugin has been developed at the National Resource for Imaging Mass Spectrometry (NRIMS, http://www.nrims.hms.harvard.edu), an NIH-supported National Resource developing Multi-isotope Imaging Mass Spectrometry (MIMS) for biomedical research. Images and/or stacks of images of up to 7 different isotopes can be opened, analyzed and saved. Image ratios and Hue-Saturation-Intensity (HSI) maps of any combination of isotopes can be displayed and data from any number of Regions of Interest (ROIs) extracted, analyzed and tabulated for single images or entire stacks. ================================== ACKNOWLEDGEMENT ================================== OpenMIMS is an Open Source software project that is funded through the NIH/NIBIB National Resource for Imaging Mass Spectrometry. Please use the following acknowledgment and send us references to any publications, presentations, or successful funding applications that make use of OpenMIMS software: "This work was made possible in part by the OpenMIMS software whose development is funded by the NIH/NIBIB National Resource for Imaging Mass Spectrometry, NIH/NIBIB 5P41 EB001974-10." ================================== HARDWARE AND SOFTWARE REQUIREMENTS ================================== OpenMIMS is an ImageJ plugin. It will run on any system running ImageJ 1.43u (or higher) and Java 1.6 (or higher). The ImageJ application can be downloaded at the following location: http://rsbweb.nih.gov/ij/download.html Additionally, due to the potentially large image sizes generated by the NanoSIMS mass spectrometer, it is suggested that approximately 2G of memory be devoted to running the ImageJ application if the OpenMIMS plugin is going to be used. This can be done by setting the maximum Java heap size flag in the "run" file used to start ImageJ, for example: java -Xmx2048m -jar ij.jar ================================== CONTENTS AND INSTALLATION ================================== To install the OpenMIMS plugin, copy the contents of the Open_MIMS.zip file into the "plugins" directory under ImageJ. Only the .jar files need to be the placed in the "plugins" directory. The files README_OpenMIMS.txt and MimsManual.pdf are documentation files and are not required by the OpenMIMS plugin. The contents of the Open_MIMS.zip file includes the following files: * jcommon-1.0.16.jar * jfreechart-1.0.13.jar * nrims_java_common.jar * Open_MIMS.jar * swing-layout-1.0.3.jar * Turbo_Reg.jar * commons-io-2.0.jar * jRtf-0.3.jar * beansbinding-1.2.1.jar * junique-1.0.4.jar * README_OpenMIMS.txt * MimsManual.pdf **IMPORTANT** Please delete any jar files that may already exist in your "plugins" directory from any older versions of the OpenMIMS plugin. Having older libraries in the "plugins" directory can cause conflicts within the software. Once the contents are copied over, restart ImageJ and "Open MIMS Image" should appear under "Plugins" menu in ImageJ. See MimsManual.pdf for a brief guide/manual on the OpenMIMS plugin. ================================== RELEASE NOTES ================================== June 2012 (v2.5): - Allow for opening of individual tiles for mosaic images. - Auto generate derived images when opening individual tiles from mosaic. - Added 3D HSI export in QVis format. - Additional functionality of Generate Report feature. - Added sanity/error check between file header and actual data in file. - More organized layout when generating Sum images. - Decimal places in table adjustable. - Read/Write metadata key value pairs. - Various performance upgrade and bug fixes. December 2011 (v2.0): - Implemented QSA and dead time correction. - All data product report raw data only (not medianized). - Performance increases in the Roi Manager (and better behavior of brush tool). - Mass symbols from .im file displayed on Mims Data tab. - Able to open plugin as a single instance. - Check for changes before opening new files. - Various performace improvements. - Changes to facilitate the api for scripting. - Fixed layout for MACs. October 2011 (v1.4x): - Various UI improvements and code cleanup. - Filter +/- infinity from plots. - Better behavior for generating tables. - Allow hsi to show up in tomography tab. - Allow users to generate reports. - Added terminal usage capability to plugin for batch jobs. - Allow user to delete columns from table. - Make opening file a background/cancelable task. - Read stage scan .im files. - Read line scan .im files. - Read 32 bit files, March 2011 (v1.4): - Added feature in RoManager allowing user to get pixel values for Rois. - Added a file filter to the open file dialog. - Status updates while opening large files. - Always update ImageJ default directory when opening or saving files of any type. - Better behavior for Rois encapsulated within a Roi. - Enable ratio images with a denominator of 1, opening up all the features for ratio images to mass images. - Fixed buggy behavior of profile plots for line Rois. - Fixed 'rename' button for renaming Rois and Roi groups. - Added the N/D statistic and enabled all statistics in the Tomography tab. - Fixed bug that prevented zooming of the x-axis on Contrast plots. - General upgrades in performace . November 2010 (v1.0): The official version 1.0 release of the OpenMIMS plugin. ================================== LICENSE INFORMATION ================================== Copyright 2010 NRIMS, National Resource for Imaging Mass Spectrometry. All rights reserved. http://www.nrims.hms.harvard.edu/ Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), copy, modify, merge, publish, or otherwise alter this software for educational or academic purposes subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. The copyright holders of other software modified and included in the Software retain their rights and the licenses on that software should not be removed. Cite the NRIMS acknowledgement (above) in any publication that relies on the Software. Also cite those projects on which the Software relies when applicable. See the "About OpenMIMS" menu for the most up to date list. If you would like to use or modify the Software for commercial purposes contact us. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. OpenMIMS has modified, uses, or depends upon: * TurboReg: http://bigwww.epfl.ch/thevenaz/turboreg/ * libSVM: http://www.csie.ntu.edu.tw/~cjlin/libsvm/ * NRRD file format: http://teem.sourceforge.net/nrrd/ * nrrd plugins: http://flybrain.stanford.edu/nrrd * jFreeChart: http://www.jfree.org/jfreechart/ * FileDrop: http://iharder.sourceforge.net/current/java/filedrop/ * Apache Commons: http://commons.apache.org/io/ * jRTF: http://code.google.com/p/jrtf/ * jUnique: http://www.sauronsoftware.it/projects/junique/ Please cite OpenMIMS or any of the above projects when applicable. ================================== CONTACT INFORMATION ================================== National Resource for Imaging Mass Spectometry Website: http://www.nrims.hms.harvard.edu Email: nrims@rics.bwh.harvard.edu Phone: (617) 768-8262 Fax: (617) 768-8260 To download the OpenMIMS plugin: http://www.nrims.harvard.edu/software.php For inquiries regarding feature requests, bug report, or anything else related to the OpenMIMS plugin, please send email to: nrims.software@rics.bwh.harvard.edu