My university has done a wonderful thing, in accepting only PDF files for deposition of a thesis or dissertation with the graduate school. Gone are the days of printing 5 copies of a 300-page document on acid-free paper that costs 20 cents a page (and then finding out that one of the margins is 0.1" too wide, so please correct and resubmit before the deadline in three hours). The transition is a wonderful step forward, and also means that it is much easier to distribute the dissertation.
As a proponent of free and open source software (having made the big switch about a year ago), I wanted to do as much as I could within the realms of that universe. This posting summarizes the software I used, with the hope of inspiring others to follow a similar path (whether in whole or in part).
Data visualization: I processed all of my CT scan data in 3D Slicer. For segmenting structures, generating surfaces, and measuring volumes, look no further! [I still need to do a more complete post on this one.] Additional analysis was done in ImageJ.
Data analysis: Initial data entry in OpenOffice.org's Calc, with analysis primarily in R and an occasional venture to PAST.
Figures: Raster image editing was done in the GIMP, and line drawings or composite figures were assembled in Inkscape.
Word processing: All done in OpenOffice.org's Writer. The PDF output function was very nice for sending drafts to committee members and advisors, and the software's Microsoft Office compatibility is such that I could also send and receive marked-up documents (in .doc format) pretty easily. For the final document, I exported each chapter in PDF format.
Referencing: All of my references were sorted, organized, and rendered as bibliographies with Zotero. Along the way, I created custom styles for Journal of Vertebrate Paleontology and Zoological Journal of the Linnean Society. More on this process in another post.
Document assembly: To assemble all of my dissertation's chapters into a single PDF document, I used Ghostscript. The output was quite pleasing, and easily accomplished through the command line in a matter of seconds.
Presentations: For my oral dissertation defense, I created my presentation using OpenOffice.org's Impress.
Showing posts with label GIMP. Show all posts
Showing posts with label GIMP. Show all posts
Friday, May 23, 2008
Tuesday, February 5, 2008
GIMP
No, this is not an unfortunate slur - it's actually an acronym for "GNU Image Manipulation Program."* And what a program it is! GIMP is one of the most mature and functional open source programs out there, and should be the first choice for anyone looking to do any sort of image editing.
GIMP is available for Windows, the Mac OS, and Linux. The closest commercial equivalent to GIMP is Adobe Photoshop - just like Photoshop, GIMP excels at editing raster images. It is under very active development, and new versions and bug fixes are constantly on their way.
As a tool for editing photographs destined for publications or presentations, you really can't beat GIMP. It has a whole host of very functional tools for selection, touch-up, and flat-out manipulation of images. Want to rotate a portion of the image? Easy enough. Need to remove a black background and replace it with white? No problem. There's not much more I can say - GIMP is fantastic! To be perfectly honest, I haven't missed Photoshop at all since making the switch (although I am sure Photoshop "power users" might disagree).
So are there any downsides to GIMP? Some users may report slow speeds, but this seems to be largely fixed in the more recent versions. For folks who may want to do extremely hard-core editing of color images for later printing, GIMP only supports RGB color formatting (although you can choose colors on the palette using CMYK standards). This may pose a problem if you want to send your files to a professional printer, but it should not affect the average user (or the paleontologist who is usually working in grayscale images). Finally, the GIMP toolbar and image editing pane open as two separate and discrete windows, rather than as subwindows within a main window (as in versions of Photoshop that I've used). This sometimes creates a cluttered editing experience, but it's more an annoyance than anything. Integration with a tablet can be a little bit of a hassle, but it works pretty flawlessly once you get it running (and I've never tried the same task in Photoshop, so I don't know how it compares in that regard).
*GNU = a type of open source software license; it has nothing to do with the African savannah.
GIMP is available for Windows, the Mac OS, and Linux. The closest commercial equivalent to GIMP is Adobe Photoshop - just like Photoshop, GIMP excels at editing raster images. It is under very active development, and new versions and bug fixes are constantly on their way.
As a tool for editing photographs destined for publications or presentations, you really can't beat GIMP. It has a whole host of very functional tools for selection, touch-up, and flat-out manipulation of images. Want to rotate a portion of the image? Easy enough. Need to remove a black background and replace it with white? No problem. There's not much more I can say - GIMP is fantastic! To be perfectly honest, I haven't missed Photoshop at all since making the switch (although I am sure Photoshop "power users" might disagree).
So are there any downsides to GIMP? Some users may report slow speeds, but this seems to be largely fixed in the more recent versions. For folks who may want to do extremely hard-core editing of color images for later printing, GIMP only supports RGB color formatting (although you can choose colors on the palette using CMYK standards). This may pose a problem if you want to send your files to a professional printer, but it should not affect the average user (or the paleontologist who is usually working in grayscale images). Finally, the GIMP toolbar and image editing pane open as two separate and discrete windows, rather than as subwindows within a main window (as in versions of Photoshop that I've used). This sometimes creates a cluttered editing experience, but it's more an annoyance than anything. Integration with a tablet can be a little bit of a hassle, but it works pretty flawlessly once you get it running (and I've never tried the same task in Photoshop, so I don't know how it compares in that regard).
*GNU = a type of open source software license; it has nothing to do with the African savannah.
Subscribe to:
Posts (Atom)