Data and code related to psychophysical assessment of color vision done at UPenn for subjects reported in Naik et al. The reader interested in digging into the phenotyping of individual subjects is encourged to consider the raw data provided here, as described below.
Subject IDs at Penn have the form MELA_XXXX where XXXX is a number. Subject IDs in the paper have form MYY, where YY is a number. The relation between these IDs is provided in spreadsheet input/ColorVisionSubject_PlatesOculus.xlsx.
Best corrected visual acuity and detailed Ishihara plate results for subjects (where available) are provided in spreadsheet data/BCVA_and_IshiharaPlates.xlxs. One additional subject, MELA_0224 was diagnosed as red-green deficient using the Ishihara plates, but the protocol used for this subject did not include recording the detailed responses. Similarly, subjects MELA_0119, MELA_0147, MELA_0153, MELA_0155, MELA_0167, MELA_0177, MELA_0179, MELA_0181, MELA_0187, MELA_0191, and MELA_3045 were all diagnosed as color normal using the Ishihara plates, but without recording of detailed responses.
We summarized the result of the plate test for each subject as "Pass", "Deutan", "Protan", or "Red-Green Deficient (unspecified)" based on the authors' judgement of the plate results. These summaries required judgement because in various ways subject responses did not always clearly conform to the patterns described in the plate instructions, or because the details of the subjects' responses were not fully recorded. These summaries do not attempt to distinguish between anomalous trichromacy and dichromacy. In the event, no subjects were summarized with a protan defect. The summaries are avalable in spreadsheet input/ColorVisionSubject_PlatesOculus.xlxs and reported in the paper.
Cambridge Research Systems Metropsis CCT Trivector test (CCTT) raw data files are provided in data/ExpCCTT for subjects for whom these are available. The Matlab program analyze/AnalyzePhenotypes.m reads these and provides a summary of results in its output file output/PhenotypeSummary.xlxs. In all cases where the subject did not pass the plates, both the protan and deutan trivector score exceeded the diagnostic criterion of 10. In three cases the tritan trivector score also exceeded the diagnostic criterion of 15. We did not entertain the possibility that these subjects were tritanopic or achromatopsic. In all cases in which a subject passed the plates, none of the trivector scores exceeded the diagnostic criteria.
Cambridge Research Systems Metropsis CCT Ellipse test (CCTT) raw data files are provided in data/ExpCCTE for subjects for whom these are available. The Matlab program analyze/AnalyzePhenotypes.m reads these and provides a summary of results in its output file output/PhenotypeSummary.xlxs. This program also fits an ellipse to the data. Plots of the data for each subject along with the fit are available in output/CCTEFigs, with the filenames containing the NIH subject number. The program classifies subjects as normal if the ratio of the major to minor axes is less than 2.5 and the area of the ellipse is less than 500e-6. In all cases in which the subject did not pass the plates, this criterion led to them being classified as having a color vision deficit; in all cases in which subjects passed the plates, these criteria led to them being classified as having normal color vision. For subjects classified as having a deficit, we classified that deficit as protan or deutan according to whether the major axis of the fit ellipse was closer to the protan or deutan confusion line in u'v' chromaticity. These lines are also shown in the plots. We did not entertain the possibility these subjects were tritanopic or achromatopsic, nor did we attempt to use the CCTE test to distinguish between anomalous trichromacy and dichromacy. In the summary output file, ellipse major axis length is given in u'v' units x 10^-5, and ellipse area in u'v' area x 10^-6. The major axis angle is given relative to the positive x-axis in degrees. The summary classification for each subject is provided in output/PhenotypeSummary.xlxs and in the paper.
Subjects who were diagnosed as red-green deficient based on the plates were studied with the Oculus HMC-Anomaloskop. Various anomaloscope protocols were used for different subjects. The raw anomaloscope data exists as PDF files that plot the matches subjects were able to make in each run in a Pitt diagram. These files are provided in data/Exp_Anomaloscope. Each file contains the matches plotted as blue squares in the Pitt diagram, interpretive regions in that diagram, and a table of summary information. The Matlab program analyze/AnalyzePhenotypes.m reads the PDF files and is able to extract the summary information. As far as we can ascertain, the coordinates of the matches are not available in the files in machine readable form, nor in other files written by the anomaloscope.
The authors summarized the results of the amomaloscope test for each subject by examing the plots of the data and using their best judgement, attempting to determine whether each subject was best characterized by a protan or deutan deficit, and whether they were anomalous trichromats or dichromats. This was not always straightforward because of inconsistency across runs or deviation of results from simple to interpret patterns of matches. The table in the paper provides these summaries, and the table output/PhenotypeSummary.xlxs provides the number of anamoloscope runs per subject, the summaries, and additional notes about the interpretation.
The MATLAB program analyze/AnalyzePhenotypes.m produces output/PhenotypeSummary.xlxs from the data files and the information in input/ColorVisionSubject_PlatesOculus.xlxs. This program relies on code freely avaliable in repositories https://github.com/Psychtoolbox-3/Psychtoolbox-3.git (PsychophysicsToolbox) and https://github.com/brainardlab/BrainardLabToolbox.git (BrainardLabToolbox). You also need to set Matlab preferences to point to the data. See example in AnalyzePhenotypes.m