OSCR

Distinct eccentricity-driven dynamics in foveal and extrafoveal visual crowding.

Code ↔ Paper

2 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 2 matches
  1. [1] § STAR★Methods › Method details › Stimuli and apparatus ↔ private/tufteaxis.m, lines 112–217 · score 0.53 · aspect ratio, horizontal, vertically, background, edge, positioned
  2. [2] § Results › Crowding in the foveola ↔ demo_004.m, lines 56–144 · score 0.50 · staircase procedure, stimuli ranged, adaptive, width, threshold

Paper

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The authors' code

MATLAB · 309 lines · 14 KB · GPL-3.0 · 1 match

  1. function tufteaxis(mmx, mmy)
  2. %TUFTEAXIS changes the coordinate axis in a Tufte style.
  3. %
  4. % inputs:
  5. % mmx [min(x), max(x)], the existing XTick are used, OR
  6. % [min(x), t1, t2, t3, max(x)], use exactly these
  7. % mmy [min(y), max(y)], the existing YTick are used, OR
  8. % [min(y), t1, t2, t3, max(y)], use exactly these
  9. %
  10. % example:
  11. % xy = randn(100,2);
  12. % mmx = [min(xy(:,1)), max(xy(:,1))];
  13. % mmy = [min(xy(:,2)), max(xy(:,2))];
  14. % scatter(xy(:,1), xy(:,2));
  15. % tufteaxis(mmx, mmy);
  16. %
  17. % note:
  18. % the current implementation should be robust against the commands:
  19. % xlim
  20. % ylim
  21. % pbaspect
  22. % daspect
  23. %
  24. % using tricks from:
  25. % http://www.mathworks.de/matlabcentral/fileexchange/43905-kozak-scatterplot
  26. % http://undocumentedmatlab.com/blog/setting-axes-tick-labels-format/
  27. %
  28. % Stefan Harmeling * 2014-02-05
  30. % (0) remove existing tufte axis
  32. %tag = sprintf('%d', gca); % old version working till 2014a
  33. % new version, adding a random tag instead of the handle tag.
  34. tag = get(gca,'Tag');
  35. if strcmp(tag,'')
  36. tag = sprintf('%d',rand);
  37. else
  38. set(gca,'Tag','');
  39. delete(findall(gcf, 'Tag', tag))
  40. setappdata(gca, 'XLimListener', []);
  41. setappdata(gca, 'YLimListener', []);
  42. setappdata(gca, 'PositionListener', []);
  43. setappdata(gca, 'PlotBoxAspectRatioModeListener', []);
  44. setappdata(gca, 'PlotBoxAspectRatioListener', []);
  45. setappdata(gca, 'DataAspectRatioModeListener', []);
  46. setappdata(gca, 'DataAspectRatioListener', []);
  47. tag = sprintf('%d',rand);
  48. end
  49. set(gca,'Tag',tag);
  50. % (0a) sort input
  51. mmx = sort(mmx);
  52. mmy = sort(mmy);
  54. % (1) modify the current ticks
  55. if length(mmx) > 2
  56. XTick = get(gca, 'XTick'); % start with the current
  57. %XTick = mmx; % take the ticks from mmx
  58. offx = (mmx(end)-mmx(1))./10;
  59. for i = 1:length(mmx)
  60. % remove to crowded ticks
  61. XTick(XTick >= mmx(i) - offx & XTick <= mmx(i) + offx) = [];
  62. end
  63. XTick(XTick<mmx(1)) = [];
  64. XTick(XTick>mmx(end)) = [];
  65. XTick = [XTick,mmx];
  66. XTick = sort(XTick);
  67. mmx = [mmx(1), mmx(end)];
  68. else
  69. XTick = get(gca, 'XTick'); % start with the current
  70. if length(XTick) > 1
  71. offx = mean(diff(XTick))/2;
  72. else
  73. offx = 0;
  74. end % avoid crowded ticks
  75. XTick(XTick <= mmx(1) + offx) = []; % remove ticks that are smaller than min+off
  76. XTick(XTick >= mmx(2) - offx) = []; % remove ticks that are large than max-off
  77. XTick = [mmx(1), XTick, mmx(2)]; % add min and max
  78. end
  79. if length(mmy) > 2
  80. XTick = get(gca, 'YTick'); % start with the current
  81. %YTick = mmy;
  82. offy = (mmy(end)-mmy(1))./10;
  83. for i = 1:length(mmy)
  84. % remove to crowded ticks
  85. YTick(YTick >= mmy(i) - offy & YTick <= mmy(i) + offy) = [];
  86. end
  87. YTick(YTick<mmx(1)) = [];
  88. YTick(YTick>mmx(end)) = [];
  89. YTick = [YTick,mmy];
  90. YTick = sort(YTick);
  91. mmy = [mmy(1), mmy(end)];
  92. else
  93. YTick = get(gca, 'YTick');
  94. if length(YTick) > 1
  95. offy = mean(diff(YTick))/2;
  96. else
  97. offy = 0;
  98. end
  99. YTick(YTick <= mmy(1) + offy) = []; % remove ticks that are smaller than min+off
  100. YTick(YTick >= mmy(2) - offy) = []; % remove ticks that are large than max-off
  101. YTick = [mmy(1), YTick, mmy(2)]; % add min and max
  102. end
  104. % (2) switch off the current axis and add some new white background
  105. switch 1
  106. case 0
  107. % for debugging purposes: check whether the new axis align with the original ones
  108. case 1
  109. %% IN THIS SETTING ALSO THE WHITE AREA BELOW THE AXIS DISAPPEARS
  110. axis off % switch off the axis
  111. case 2
  112. %% WARNING THIS CASE LEADS TO GHOSTS IN PRINTOUTS
  113. box off % no box
  114. grid off % no grid
  115. set(gca, 'XTick', XTick); % change the ticks
  116. set(gca, 'YTick', YTick);
  117. set(gca, 'TickDir', 'out'); % the ticks should point out, otherwise we can not hide them
  118. Color = get(gcf, 'Color'); % get background color of the figure
  119. set(gca, 'XColor', Color); % hide the ticks and the axis
  120. set(gca, 'YColor', Color);
  121. end
  123. % (4) create conversion functions
  124. XLim = get(gca, 'XLim'); % get the coordinate system
  125. YLim = get(gca, 'YLim'); % get the coordinate system
  126. XLim = [min(mmx(1), XLim(1)), max(mmx(2), XLim(2))]; % increase limits if necessary
  127. YLim = [min(mmy(1), YLim(1)), max(mmy(2), YLim(2))]; % increase limits if necessary
  128. if strcmp(get(gca,'XScale'), 'linear')
  129. XLim(1) = min(XLim(1), mmx(1) - 0.1*(mmx(2)-mmx(1))); % to avoid points on the axis
  130. else %logspace
  131. XLim(1) = min(XLim(1), exp(log(mmx(1)) - 0.1*(log(mmx(2))-log(mmx(1)))));
  132. end
  133. if strcmp(get(gca,'YScale'), 'linear')
  134. YLim(1) = min(YLim(1), mmy(1) - 0.1*(mmy(2)-mmy(1))); % to avoid points on the axis
  135. else
  136. YLim(1) = min(YLim(1), exp(log(mmy(1)) - 0.1*(log(mmy(2))-log(mmy(1)))));
  137. end
  138. set(gca, 'XLim', XLim);
  139. set(gca, 'YLim', YLim);
  140. [left, bottom, width, height] = calcLimits(gca);
  141. if strcmp(get(gca,'XScale'), 'linear')
  142. tx = @(x) left + width * (x - XLim(1)) / diff(XLim); % convert to global position
  143. else % logscale
  144. tx = @(x) left + width * (log(x) - log(XLim(1))) / diff(log(XLim)); % convert to global position
  145. end
  146. if strcmp(get(gca,'YScale'), 'linear')
  147. ty = @(y) bottom + height * (y - YLim(1)) / diff(YLim); % convert to global position
  148. else % logscale
  149. ty = @(y) bottom + height * (log(y) - log(YLim(1))) / diff(log(YLim)); % convert to global position
  150. end
  152. % (5) draw new axis
  153. ax = annotation('line', tx(mmx), bottom*[1,1]); % x coordinate axis
  154. ay = annotation('line', left*[1,1], ty(mmy)); % y coordinate axis
  156. % (6) draw new ticks
  157. gcfpos = get(gcf, 'Position');
  158. ticklength = 7; % in pixel
  159. xticklength = ticklength / gcfpos(4); % in pixel / "number of vertical pixels"
  160. yticklength = ticklength / gcfpos(3); % in pixel / "number of horizontal pixels"
  161. nXTick = length(XTick);
  162. ttx = zeros(nXTick, 1); % to store ticks
  163. tlx = zeros(nXTick, 1); % to store labels
  164. for i = 1:nXTick
  165. ttx(i) = annotation('line', tx(XTick(i)*[1,1]), bottom-[0, xticklength]);
  166. tlx(i) = annotation('textbox', [tx(XTick(i)), bottom-xticklength, 0, 0], ...
  167. 'string', num2str(XTick(i),'%.3g'), ...
  168. 'VerticalAlignment', 'top', ...
  169. 'HorizontalAlignment', 'center', ...
  170. 'EdgeColor', 'none',...
  171. 'FontSize',get(gca,'FontSize'));
  172. end
  173. nYTick = length(YTick);
  174. tty = zeros(nYTick, 1); % to store ticks
  175. tly = zeros(nYTick, 1); % to store labels
  176. for i = 1:length(YTick)
  177. tty(i) = annotation('line', left-[0, yticklength], ty(YTick(i)*[1,1]));
  178. tly(i) = annotation('textbox', [left-yticklength, ty(YTick(i)), 0, 0], ...
  179. 'string', num2str(YTick(i),'%.3g'), ...
  180. 'VerticalAlignment', 'middle', ...
  181. 'HorizontalAlignment', 'right', ...
  182. 'EdgeColor', 'none',...
  183. 'FontSize',get(gca,'FontSize'));
  184. end
  185. for h = [ax; ttx(:); tlx(:); ay; tty(:); tly(:)]'
  186. set(h, 'Tag', tag); % mark the annotations to find them on our next
  187. % call using axis specific tag should make
  188. % this compatible with SUBPLOT
  189. end
  191. % (7) and now some magic tricks (to auto update the axis after
  192. % changing parameters via XLIM, YLIM, DASPECT, PBASPECT)
  193. hhAxes = handle(gca); % gca is the Matlab handle of our axes
  195. hProp = findprop(hhAxes,'XLim'); % a schema.prop object
  196. hListener = handle.listener(hhAxes, hProp, 'PropertyPostSet', @updateAxis);
  197. setappdata(gca, 'XLimListener', hListener);
  198. hProp = findprop(hhAxes,'YLim'); % a schema.prop object
  199. hListener = handle.listener(hhAxes, hProp, 'PropertyPostSet', @updateAxis);
  200. setappdata(gca, 'YLimListener', hListener);
  201. hProp = findprop(hhAxes,'Position'); % a schema.prop object
  202. hListener = handle.listener(hhAxes, hProp, 'PropertyPostSet', @updateAxis);
  203. setappdata(gca, 'PositionListener', hListener);
  204. hProp = findprop(hhAxes,'PlotBoxAspectRatioMode'); % a schema.prop object
  205. hListener = handle.listener(hhAxes, hProp, 'PropertyPostSet', @updateAxis);
  206. setappdata(gca, 'PlotBoxAspectRatioModeListener', hListener);
  207. hProp = findprop(hhAxes,'PlotBoxAspectRatio'); % a schema.prop object
  208. hListener = handle.listener(hhAxes, hProp, 'PropertyPostSet', @updateAxis);
  209. setappdata(gca, 'PlotBoxAspectRatioListener', hListener);
  210. hProp = findprop(hhAxes,'DataAspectRatioMode'); % a schema.prop object
  211. hListener = handle.listener(hhAxes, hProp, 'PropertyPostSet', @updateAxis);
  212. setappdata(gca, 'DataAspectRatioModeListener', hListener);
  213. hProp = findprop(hhAxes,'DataAspectRatio'); % a schema.prop object
  214. hListener = handle.listener(hhAxes, hProp, 'PropertyPostSet', @updateAxis);
  215. setappdata(gca, 'DataAspectRatioListener', hListener);
  217. % (8) helper functions
  219. function [left, bottom, width, height] = calcLimits(axisHandle)
  220. % calculate the correct positions of the axes depending on
  221. % 'Position'
  222. % 'PlotBoxAspectRatioMode', 'PlotBoxAspectRatio'
  223. % 'DataAspectRatioMode', 'DataAspectRatio'
  224. % 'CameraViewAngleMode', 'CameraViewAngle'
  225. OrigUnits = get(gcf, 'Units');
  226. set(gcf, 'Units', 'pixels');
  227. fpos = get(gcf, 'Position'); % left, bottom, width, height
  228. factor = fpos(3)/fpos(4); % ratio between width and height
  229. set(gcf, 'Units', OrigUnits);
  230. pos = get(axisHandle, 'Position');
  231. left = pos(1); bottom = pos(2); width = pos(3); height = pos(4);
  232. if strcmp(get(gca, 'PlotBoxAspectRatioMode'), 'manual') || strcmp(get(gca, 'DataAspectRatioMode'), 'manual')
  233. % PlotBoxAspectRatio influences the exact position
  234. % curiously for DataAspectRatioMode the following also works
  235. pbar = pbaspect();
  236. pbar12 = pbar(1)/pbar(2)/factor;
  237. wh = width/height;
  238. if pbar12 < wh
  239. % adjust left and width
  240. widthnew = height * pbar12;
  241. left = left + width/2 - widthnew/2;
  242. width = widthnew;
  243. elseif pbar12 > wh
  244. % adjust bottom and height
  245. heightnew = width / pbar12;
  246. bottom = bottom + height/2 - heightnew/2;
  247. height = heightnew;
  248. end
  249. end
  250. if strcmp(get(gca, 'CameraViewAngleMode'), 'manual')
  251. error('manual CameraViewAngleMode not support yet')
  252. end
  253. end
  256. function updateAxis(hProp,eventData)
  257. XLim = get(eventData.AffectedObject, 'XLim'); % get the coordinate system
  258. YLim = get(eventData.AffectedObject, 'YLim'); % get the coordinate system
  259. [left, bottom, width, height] = calcLimits(eventData.AffectedObject);
  260. if strcmp(get(eventData.AffectedObject,'XScale'), 'linear')
  261. tx = @(x) left + width * (x - XLim(1)) / diff(XLim); % convert to global position
  262. else % logscale
  263. tx = @(x) left + width * (log(x) - log(XLim(1))) / diff(log(XLim)); % convert to global position
  264. end
  265. if strcmp(get(eventData.AffectedObject,'YScale'), 'linear')
  266. ty = @(y) bottom + height * (y - YLim(1)) / diff(YLim); % convert to global position
  267. else % logscale
  268. ty = @(y) bottom + height * (log(y) - log(YLim(1))) / diff(log(YLim)); % convert to global position
  269. end
  270. set(ax, 'X', max(min(tx(mmx), left+width), left));
  271. set(ax, 'Y', bottom*[1,1]);
  272. for i = 1:nXTick
  273. XTicki = XTick(i);
  274. if XTicki < XLim(1) || XLim(2) < XTicki
  275. set(ttx(i), 'Visible', 'off');
  276. set(tlx(i), 'Visible', 'off');
  277. else
  278. set(ttx(i), 'Visible', 'on');
  279. set(tlx(i), 'Visible', 'on');
  280. thex = tx(XTicki);
  281. set(ttx(i), 'X', thex*[1,1]);
  282. set(ttx(i), 'Y', bottom-[0,xticklength]);
  283. tlxPos = get(tlx(i), 'Position');
  284. tlxPos(1) = thex;
  285. tlxPos(2) = bottom-xticklength;
  286. set(tlx(i), 'Position', tlxPos);
  287. end
  288. end
  289. set(ay, 'X', left*[1,1]);
  290. set(ay, 'Y', max(min(ty(mmy), bottom+height), bottom));
  291. for i = 1:nYTick
  292. YTicki = YTick(i);
  293. if YTicki < YLim(1) || YLim(2) < YTicki
  294. set(tty(i), 'Visible', 'off');
  295. set(tly(i), 'Visible', 'off');
  296. else
  297. set(tty(i), 'Visible', 'on');
  298. set(tly(i), 'Visible', 'on');
  299. they = ty(YTicki);
  300. set(tty(i), 'X', left-[0,yticklength]);
  301. set(tty(i), 'Y', they*[1,1]);
  302. tlyPos = get(tly(i), 'Position');
  303. tlyPos(1) = left-yticklength;
  304. tlyPos(2) = they;
  305. set(tly(i), 'Position', tlyPos);
  306. end
  307. end
  308. end
  309. end

tufteaxis.m at commit 5f7241f, under GPL-3.0 · at the source

Overview

Authors: Ashley M Clark1,2, Krishnamachari S Prahalad1,2, Martina Poletti1,2,3
ORCID iDs: Martina Poletti
  1. Department of Brain and Cognitive Sciences, University of Rochester, Meliora Hall, Rochester, NY 14627, USA
  2. Center for Visual Science, University of Rochester, 361 Meliora Hall, Rochester, NY 14627, USA
  3. Department of Neuroscience, University of Rochester, 601 Elmwood Avenue, Rochester, NY 14642, USA
Institutions: University of Rochester (United States); University of Rochester Medicine (United States)
Journal: iScience, volume 29, issue 4, article 115168
Dates: received 25 September 2025; accepted 24 February 2026; published online 2 March 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1016/j.isci.2026.115168 · PMID 41858623 · PMCID PMC12995875 · OpenAlex W7133220886
Open access: gold, a free copy (OpenAlex)
Status: code verified
Methods: Statistics, Physiology & signal measures
Keywords: Ophthalmology, Neuroscience
Topic: Visual perception and processing mechanisms (Cognitive Neuroscience, Neuroscience), according to OpenAlex
Funding: NEI NIH HHS (R01 EY029788, P30 EY001319); National Institutes of Health
Citations: not cited yet (Europe PMC); 96 references in the paper

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Repository

Its files are read in the Code ↔ Paper reader above, with 2 matches between paragraphs and lines of code.

wichmann-lab/psignifit

License: GPL-3.0
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Commit: 5f7241f6288c7dd3e1b34353118ca919ad28e51b, 4 January 2025
Languages: MATLAB (57)
Size: 129 files, 57 scripts
Software Heritage: archived
Found in: the resources table
Holds: README, license file, tests
Not found: CITATION.cff, environment file, continuous integration, documentation
Tools: psignifit (13 files), Statistics and Machine Learning Toolbox (2 files), Optimization Toolbox (1 file), Parallel Computing Toolbox (1 file)
Availability: 1 check, the latest on 30 September 2026: the link answers
  • 30 September 2026: the link answers
59 files
At the source: github.com/wichmann-lab/psignifit

The paper's code and data availability statement is in the Data section.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 57 scripts, each with its path and the digest of its content;
  • 2 matches between paragraphs of the paper and lines of the code (method lexical-v1);
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

Datasets cited

Code and data availability statement

The paper has a code and data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

  • it points to a dataset: OSF e9k6q
  • it says that the data are available on request
  • it says that the code is available on request

Read it in the paper: doi.org/10.1016/j.isci.2026.115168.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 30 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 3 authors, 2 keywords, 2 funders, 87 references.

Cite

This paper

Clark, A. M., Prahalad, K. S., & Poletti, M. (2026). Distinct eccentricity-driven dynamics in foveal and extrafoveal visual crowding. iScience, 29(4), 115168. https://doi.org/10.1016/j.isci.2026.115168

BibTeX

@article{clark2026distinct,
author = {Clark, Ashley M and Prahalad, Krishnamachari S and Poletti, Martina},
title = {{Distinct eccentricity-driven dynamics in foveal and extrafoveal visual crowding}},
journal = {iScience},
year = {2026},
month = mar,
volume = {29},
number = {4},
pages = {115168},
publisher = {Elsevier},
issn = {2589-0042},
doi = {10.1016/j.isci.2026.115168},
url = {https://doi.org/10.1016/j.isci.2026.115168},
pmid = {41858623},
pmcid = {PMC12995875}
}

RIS

TY - JOUR
AU - Clark, Ashley M
AU - Prahalad, Krishnamachari S
AU - Poletti, Martina
TI - Distinct eccentricity-driven dynamics in foveal and extrafoveal visual crowding
T2 - iScience
J2 - iScience
PY - 2026
DA - 2026/03/02
VL - 29
IS - 4
SP - 115168
SN - 2589-0042
PB - Elsevier
DO - 10.1016/j.isci.2026.115168
UR - https://doi.org/10.1016/j.isci.2026.115168
LA - en
ER -

CSL-JSON

{
"id": "10.1016/j.isci.2026.115168",
"type": "article-journal",
"title": "Distinct eccentricity-driven dynamics in foveal and extrafoveal visual crowding",
"container-title": "iScience",
"author": [
{
"family": "Clark",
"given": "Ashley M"
},
{
"family": "Prahalad",
"given": "Krishnamachari S"
},
{
"family": "Poletti",
"given": "Martina"
}
],
"container-title-short": "iScience",
"volume": "29",
"issue": "4",
"page": "115168",
"DOI": "10.1016/j.isci.2026.115168",
"PMID": "41858623",
"PMCID": "PMC12995875",
"ISSN": "2589-0042",
"publisher": "Elsevier",
"URL": "https://doi.org/10.1016/j.isci.2026.115168",
"language": "en",
"issued": {
"date-parts": [
[
2026,
3,
2
]
]
}
}

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