/ jansonius / scientific software

Choices in scientific software

Research money should preferably be used for research - software licences belong to the eighties of the previous century. Also, performing up-to-date science should be possible without being forced to buy a new computer every five years. Below, some open source and freeware solutions are given. Linux is the primary platform. However, all proposed software packages also have a Windows port or are native Windows packages that can be used in Linux through Wine. This facilitates collaboration.

Main functionality

• OpenOffice or LibreOffice: Word/Excel/Powerpoint compatibility
• LaTeX (no need to specify)
• Octave: Matlab compatibility
• R: program for statistical computing and plotting (start with reading "Statistics - an introduction using R" by M.J. Crawley; to get a quick impression, view this tutorial)

Other free statistical programs

• NJSTAT: rather complete statistical program for DOS, Linux, ChromeOS, and Windows
• WINPEPI: pretty complete swiss army knife for statistics

LibreOffice, Octave, R, and Wine are readily available in, for example, Ubuntu Linux.

Software and data related to my scientific publications

• CHIASM: program for analysing chiasmal misrouting from VEP (supplement to: Jansonius et al (2001) J Neuro-Ophthalmology 21:26-29)
• JOA10NJA: program for calculating optical variables relevant to visual perception from wave-front analysis data (supplement to: Jansonius (2010) J Opt Soc Am A 27:941-950)
• HOA2OPT: program for estimating optical metrics from summary wave-front analysis data in the human eye (extension of JOA10NJA; supplement to Jansonius (2013) Ophthalmic Physiol Opt 33:35-41)
• plottraject.m: matlab/octave code for plotting the Jansonius retinal nerve fiber bundle trajectory map (described in: Jansonius et al (2009) Vision Res 49:2157-2163, Jansonius et al (2012) Exp Eye Res 105:70-78, Qiu et al (2015) Invest Ophthalmol Vis Sci 56:6320-5, Qui et al (2018) Exp Eye Res 176:103-109, Jansonius and Schiefer (2020) TVST 9(11):3)
• Annotated fundus pictures: 1712 fundus pictures with annotated optic disc margin and cup (supplement to: Guo et al (2019) IEEE Access 7:8527-8541, doi: 10.1109/ACCESS.2018.2890544)

Other ophthalmic software

• PERISIM: program for simulating standard automated perimetry on a regular computer
• SUPRASIM: program for simulating suprathreshold perimetry on a regular computer
• CYLINDER: program for calculations on astigmatism
• D15: program for analysing the Farnsworth D-15 (colour vision) test
• csf.m: matlab/octave code for measuring a contrast sensitivity function (described in: Bierings RAJM, Overkempe T, van Berkel CM, Kuiper M, Jansonius NM (2019) Spatial contrast sensitivity from star to sunlight in healthy subjects and patients with glaucoma. Vision research 158: 31-39)

Old scientific software - still running - C:\>

Sometimes, it is convenient to use old software - it avoids waste of time during the mastering of yet another program. Also, old files may contain highly valuable data - but only if you are able to read them. Many of the DOS programs as presented below are stripped down versions of the original software, dating back to the time I was using an XT with 20 Mb HD (16-bit), and, later, a 386 with 120 Mb HD (32-bit). The programs are, however, still fully functional. The 16-bit programs run flawlessly in DOSBox, a DOS emulator available for Linux and Windows; the 32-bit programs are nowadays sometimes more challenging.

• ChiWriter: printing and PDF output from ChiWriter (a homemade solution; 16-bit)
• GnuPlot: scientific plotting program (including several homemade additions; 16-bit and 32-bit)
• Compilers for DOS: no science without programming (16-bit and 32-bit)
• Editor ZED: DOS editor (userfriendly due to homemade configuration file; 16-bit)
• ASYST: extremely powerful ancestor of matlab (16-bit)