Frequently Asked Questions

  • Can I modify or redistribute COSMOS?

The COSMOS package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. COSMOS is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

  • How do I debug a process if a run time error occurs?

All compile time error and comments show up in the command prompt. So going back the cause of the error can be found out. This is particularly important when there are multiple iterations being implemented and an error occurs.

  • Can a file in .tiff format be read by the COSMOS?

No, but it can be converted to the .wu format using the COSMOS Tools, which can open several different formats. Only .wu format files (i.e. images with a 1024 washu header) can be read by the other applications which are a part of the COSMOS package. Images with no header are usually named with a .raw extension, which can be read by the add header tab in Cosm Tools. This tab adds the washu header and converts the file to .wu extension.

  • What are the system requirements?

13MB of Hard Disc space is required. COSMOS can run on a variety of Operating Systems.

  • Is it possible to process a 2-D image using the LLS or EM algorithms? If so, how are the parameters set in the "COSM PSF" menu?

Yes, the number of planes in Z equal to 1. The rest of the parameters are kept as it is.

  • If images are saturated can they still be processed with the COSMOS algorithms?

Yes, the intensities will be scaled down, but it can easily be processed with some losses.

  • What does "pixel size in object space" in the "Generate PSF" menu mean?

Is it the size of a single element of the CCD camera or the size of a single pixel of the image acquired by the CCD camera? Pixel size in object space is equal to the physical CCD pixel size divided by the magnification of all the lenses between the specimen and the camera. For most microscopes, the only lens between the specimen and the camera is the objective lens. For other microscopes, there may be an additional relay lens that further magnifies the image to the camera.

  • When I publish results generated with COSMOS, which of your papers should I reference, and how do I cite the COSMOS package?

COSMOS citations should be made by referring to the COSMOS web page (http://cirl.memphis.edu/cosmos). In addition, depending on which algorithm you used to process your images you should cite the publication describing the algorithm. A list of all the algorithms implemented in COSMOS and the references for each algorithm are provided at the COSMOS web page.