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StereoPylot: An Open-Source Raspberry Pi-Based Stereotaxic Apparatus Controller with 3D Printed Components for Fully Motorized Control, Digital Display, and Customizable Features.

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 · all tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
  1. [1] § Materials and Methods › Assembly of the upper control box ↔ LeftHand/VariableList.py, the whole file · a weak match · score 0.53 · shift registers, rotary encoders, pins, switch, wiring, buttons
  2. [2] § Materials and Methods › Assembly of the upper control box ↔ RightHand/VariableList.py, the whole file · a weak match · score 0.53 · shift registers, rotary encoders, pins, switch, wiring, buttons

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

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The authors' code

Python · 247 lines · 5.7 KB · GPL-3.0 · 1 match

  1. class var_list:
  3. #From UI
  4. countoflistwidget = 0
  5. list_toggle = 9999
  7. #FROM BUTTONCLASS *********************************************************
  9. #Main while loop condition
  10. keepalive = True
  12. #Stepper instances
  13. APmove = None
  14. MLmove = None
  15. DVmove = None
  16. AUXmove = None
  19. # OFFSETS FOR THE DRILL, Syringe, Needle (minus values is back, left or up)
  20. # in mm using the drill as 0
  22. # Change in the file offsetsXX.txt (XX is LH or RH)
  23. DrillAPmm = float(0)
  24. DrillMLmm = float(0)
  25. DrillDVmm = float(0)
  27. NeedleAPmm = float(11.1)
  28. NeedleMLmm = float(-31.22)
  29. NeedleDVmm = float(5)
  31. FiberAPmm = float(-5.069)
  32. FiberMLmm = float(31.22)
  33. FiberDVmm = float(1.1)
  35. # variable to let program know which offset of toggled on. 1-drill,2-syringe,3-probe
  36. TOGGLEoff = 1
  37. offtoggleold = 1
  39. # DEFINE NUMBER OF BUTTONS AND ORDER IN ARRAY
  40. buttonarray = ['DVinsert', 'withdrawl', 'fullretract', 'rezero', 'bregmahomeDVupfive',
  41. 'bregmahomeDVabs', 'ABSzero', 'gotopreset', 'makeitsobut', 'engagebut',
  42. 'selectdown', 'selectup', 'retractAP', 'returnAP', 'bregmahome',
  43. 'gotolambdabut', 'ratselect', 'mouseselect', 'functionone', 'armbut',
  44. 'relativeML', 'retractDV', 'returnDV', 'functiontwo', 'relativeAP',
  45. 'relativeALLset', 'offpostwo', 'offposone', 'unassigned', 'movefast', 'moveslow',
  46. 'relativeDV']
  48. lastbuttonstate = [0 for x in range(len(buttonarray))]
  50. # BUTTON POSITION IN SHIFT REGISTER ARRAY (0 to 31)
  51. moveslow = 30
  52. movefast = 29
  53. offposone = 27
  54. offpostwo = 26
  55. rezero = 3
  57. relativeAP = 24
  58. relativeML = 20
  59. relativeDV = 31
  60. relativeALL = 25
  61. fullretractbut = 2
  63. bregmahome = 14
  64. bregmahomeDVabs = 5
  65. bregmahomeDVupfive = 4
  66. gotolambdabut = 15
  67. ratselect = 16
  69. mouseselect = 17
  70. gotopreset = 7
  71. selectup = 11
  72. selectdown = 10
  73. armbut = 19
  75. engagebut = 9
  76. makeitsobut = 8
  77. withdrawl = 1
  78. DVinsert = 0
  79. retractAP = 12
  81. returnAP = 13
  82. retractDV = 21
  83. returnDV = 22
  84. functionone = 18
  85. functiontwo = 23
  87. ABSzero = 6
  89. #DEFINE EMERGENCY STOP and hard wired buttons GPIO
  90. emergstop = 26
  91. safetybut = 9
  92. disablestepperbut = 10
  93. fourthhardwarebutton = 11 #encoder 4 depress?
  95. #DEFINE SHIFT REGISTER PINS
  96. latchpin = 18
  97. clockpin = 23
  98. datapin = 24
  100. #DEFINE STEPPER SPEEDS - number of steps per call
  101. finespeed = 1
  102. normalspeed = 10
  103. fastspeed = 50
  105. #stepper_speed initializes as 1 BUT changes according to the state of the speed switch
  106. stepper_speed = finespeed
  108. #FROM StepperControl class *********************************************************
  109. btnSteps = 0.001
  111. APsteps = 0
  112. MLsteps = 0
  113. DVsteps = 0
  114. AUXsteps = 0
  116. APrelpos = 0
  117. MLrelpos = 0
  118. DVrelpos = 0
  120. APretractstart = 0
  121. DVretractstart = 0
  124. DVinitREL_holdvalue = 0
  125. MLinitREL_holdvalue = 0
  126. APinitREL_holdvalue = 0
  128. DVcurrentoffsset = 0
  129. MLcurrentoffsset = 0
  130. APcurrentoffsset = 0
  132. APstepdistance = float(0.0075)
  133. MLstepdistance = float(0.0075)
  134. DVstepdistance = float(0.0075)
  136. APcurABSdist = float(0)
  137. MLcurABSdist = float(0)
  138. DVcurABSdist = float(0)
  140. APcurRELdist = float(0)
  141. MLcurRELdist = float(0)
  142. DVcurRELdist = float(0)
  144. #FROM Threadedcontrol class *********************************************************
  146. #Variables that may need tweaking
  147. calibrationsteps = 4000
  148. backoff = 50 #200
  149. APadvance = 2000 #2000
  150. DVadvance = 400 #400
  151. MLadvance = 400 #400
  153. APworking = 6400
  154. MLworking = 6070
  155. DVworking = 3500
  157. fullretract = 7650
  158. fullretractML = 9500
  160. DVup_bregramhome = 268 #about 0.2cm
  161. DVup_lambdabregma = 200 # about 0.15cm
  162. DVup_five = 675 # about 5 mm
  164. # how many steps DV goes up and then back when changing the offsets to avoid scrapping the skull
  165. DVup_OffsetSafety = 1340 #about 1 cm
  168. #DEFINE STEPPER CONTROL PINS
  169. enableAll = 2
  171. directionAP = 3
  172. stepAP = 4
  174. directionML = 17
  175. stepML = 27
  177. directionDV = 5
  178. stepDV = 6
  180. directionAUX = 1
  181. stepAUX = 7
  183. #DEFINE LIMIT SWITCH PINS
  184. limitAP = 22
  185. limitML = 19
  186. limitDV = 0
  187. limitAUX = 13
  189. #DEFINE ROTARY ENCODER PINS
  190. rotoA_AP = 21
  191. rotoB_AP = 20
  192. rotoA_ML = 12
  193. rotoB_ML = 16
  194. rotoA_DV = 8
  195. rotoB_DV = 25
  196. rotoA_fourth = 14
  197. rotoB_fourth = 15
  199. #ENCODER CALC VARIABLES
  200. eventime = 0
  201. eventdelay = 200
  202. backwardrotdelay = 400
  203. lastdirection = 0 #3 = counterclock, 1 = clock
  204. thecount = 0
  205. firstandonly = 0
  207. #DEFINE STEPPER DIRECTIONS
  208. APback = 1
  209. APforward = 0
  210. MLleft = 1
  211. MLright = 0
  212. DVup = 0
  213. DVdown = 1
  214. AuxUP = 0
  215. AuxDown = 1
  217. calibfilename = 'CalibrationLH.txt'
  218. offsetfilename = 'offsetsLH.txt'
  220. lastenablestate = 1
  221. emergencystopflag = 0
  222. engagebutton = 0
  223. safetybutton = 0
  225. withdrawinsertstop = 0
  226. dvinsertstop = 0
  228. DVinsertindicator = 0
  229. Withdrawlindicator = 0
  230. Makeitsoindicator = 0
  233. ratormouseselect = 1 #1 is mouse 2 is rat 3 is null(mouse default)
  234. ratlambda = 1208 # steps for 9mm at 0.0745 per step
  235. mouselambda = 550 # steps for 4.1mm at 0.0745 per step
  236. rellambda = 0
  238. # For timerthread safety timeouts
  239. timeoutlength = 3
  242. DVinserttimeouttime = None
  243. Safetytimeouttime = None
  244. Withdrawltimeouttime = None
  245. Makeitsobuttimeouttime = None
  247. # concept and code created by Kirk Mulatz (original code https://github.com/bustenchops/Stereotaxiccontrol (experiment branch)

VariableList.py at commit db7209a, under GPL-3.0 · at the source

Overview

Authors: Kirk Mulatz1, Aiden E. Glass1, McKenna A. Bolger1, Caleb L. G. White1, John G. Howland1, Justin J. Botterill1
ORCID iDs: John G. Howland, Justin J. Botterill
  1. Department of Anatomy, Physiology, and Pharmacology, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
Institutions: University of Saskatchewan (Canada)
Journal: eNeuro, volume 13, issue 7, pages ENEURO.0460-25.2026
Dates: received 11 December 2025; accepted 15 June 2026; published online 7 July 2026; in print July 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1523/eneuro.0460-25.2026 · PMID 42331622 · PMCID PMC13362190 · OpenAlex W7165559118
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: rat (organism), methods / tools (subfield)
Methods: Statistics
Keywords: 3D printing, adeno-associated virus, anatomy, brain, neuroscience, Raspberry Pi, stereotaxic apparatus
MeSH: Brain*, Printing, Three-Dimensional*, Stereotaxic Techniques*, Animals, Equipment Design, Female, Male, Software (* major topic)
Journal subjects: Research Article: Methods/New Tools, Novel Tools and Methods
Topic: Neurological disorders and treatments (Neurology, Medicine), according to OpenAlex
Funding: Natural Sciences and Engineering Research Council of Canada; University of Saskatchewan College of Medicine
Citations: not cited yet (Europe PMC); 26 references in the paper

Abstract

Stereotaxic surgery is a powerful technique used to deliver drugs, viral vectors, and/or probes into discrete regions of the brain. Over the past decade, the emphasis on performing complex surgeries for neural circuit manipulations or studying multiple brain regions in the same animal has increased. While analog stereotaxic instruments are generally suitable for these types of experiments, the surgeon must accurately read vernier scales for each brain region of interest, which is both time-consuming and prone to user error. Although vendors now offer digital stereotaxic instruments that overcome the limitations of analog instruments, digital units are cost-prohibitive and often come in limited configurations that lack clear paths to customize or upgrade as experimental needs change. To overcome these issues, we've created StereoPylot, an open-source Raspberry Pi-based stereotaxic controller with 3D-printed components. StereoPylot features motorized control of X-, Y-, and Z-axes, variable motor speed, programmable buttons, and a digital display for stereotaxic coordinates. We also created a custom graphical user interface which allows surgeons to move the manipulators to an area of interest by manually entering stereotaxic coordinates on screen or by loading a preset file that contains a list of user-defined stereotaxic coordinates. We demonstrate practical application of StereoPylot by quantifying viral expression in three male and three female Long–Evans rats and provide instrument accuracy and precision measurements. StereoPylot is therefore feature-rich and highly customizable while being relatively inexpensive to implement onto existing analog instruments commonly found in neuroscience laboratories.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repository

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

botterillneurolab/StereoPylot

License: GPL-3.0
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: db7209a313dc6a21e145f5616096a121ed564a92, 23 April 2026
Languages: Python (19), Shell (2)
Size: 62 files, 21 scripts
Software Heritage: not archived
Found in: “Code accessibility”
Holds: license file, environment (Requirements/localrequirements.txt, Requirements/requirements.txt)
Not found: README, CITATION.cff, tests, continuous integration, documentation
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
22 files
At the source: github.com/botterillneurolab/StereoPylot

Code accessibility

The code and software described in the paper is freely available online at https://github.com/botterillneurolab/StereoPylot

Reproduced under the paper's license (CC BY), from the paper cited above.

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;
  • 21 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

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Versions

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Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 6 authors, 7 keywords, 8 MeSH terms, 2 funders, 24 references.

Cite

This paper

Mulatz, K., Glass, A. E., Bolger, M. A., White, C. L. G., Howland, J. G., & Botterill, J. J. (2026). StereoPylot: An Open-Source Raspberry Pi-Based Stereotaxic Apparatus Controller with 3D Printed Components for Fully Motorized Control, Digital Display, and Customizable Features. eNeuro, 13(7), ENEURO.0460-25.2026. https://doi.org/10.1523/eneuro.0460-25.2026

BibTeX

@article{mulatz2026stereopylot,
author = {Mulatz, Kirk and Glass, Aiden E. and Bolger, McKenna A. and White, Caleb L. G. and Howland, John G. and Botterill, Justin J.},
title = {{StereoPylot: An Open-Source Raspberry Pi-Based Stereotaxic Apparatus Controller with 3D Printed Components for Fully Motorized Control, Digital Display, and Customizable Features}},
journal = {eNeuro},
year = {2026},
month = jul,
volume = {13},
number = {7},
pages = {ENEURO.0460--25.2026},
publisher = {Society for Neuroscience},
issn = {2373-2822},
doi = {10.1523/eneuro.0460-25.2026},
url = {https://doi.org/10.1523/eneuro.0460-25.2026},
pmid = {42331622},
pmcid = {PMC13362190}
}

RIS

TY - JOUR
AU - Mulatz, Kirk
AU - Glass, Aiden E.
AU - Bolger, McKenna A.
AU - White, Caleb L. G.
AU - Howland, John G.
AU - Botterill, Justin J.
TI - StereoPylot: An Open-Source Raspberry Pi-Based Stereotaxic Apparatus Controller with 3D Printed Components for Fully Motorized Control, Digital Display, and Customizable Features
T2 - eNeuro
J2 - eNeuro
PY - 2026
DA - 2026/07/10
VL - 13
IS - 7
SP - ENEURO.0460
EP - 25.2026
SN - 2373-2822
PB - Society for Neuroscience
DO - 10.1523/eneuro.0460-25.2026
UR - https://doi.org/10.1523/eneuro.0460-25.2026
LA - en
ER -

CSL-JSON

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"type": "article-journal",
"title": "StereoPylot: An Open-Source Raspberry Pi-Based Stereotaxic Apparatus Controller with 3D Printed Components for Fully Motorized Control, Digital Display, and Customizable Features",
"container-title": "eNeuro",
"author": [
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"family": "Mulatz",
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"container-title-short": "eNeuro",
"volume": "13",
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"PMID": "42331622",
"PMCID": "PMC13362190",
"ISSN": "2373-2822",
"publisher": "Society for Neuroscience",
"URL": "https://doi.org/10.1523/eneuro.0460-25.2026",
"language": "en",
"issued": {
"date-parts": [
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2026,
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10
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]
}
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