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The prefrontal cortex controls memory organization in the hippocampus.

Code ↔ Paper

4 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 4 matches · 2 of them tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
  1. [1] § Methods › Miniscope analysis ↔ Separate Steps/runConcatStep1.m, the whole file · a weak match · score 0.82 · NoRMCorre, rigid registration, spatially downsampled, motion correction, animal, pipeline
  2. [2] § Methods › Miniscope analysis ↔ Separate Steps/runConcatStep1.m, the whole file · a weak match · score 0.81 · NoRMCorre, rigid registration, spatially downsampled, motion correction, animal, pipeline
  3. [3] § Methods › Miniscope analysis ↔ MatlabPath_CNMFe_and_NoRMCorre/@Sources2D/Sources2D.m, lines 9–57 · score 0.73 · quality control, noise ratio, calcium transients, peak, deconvolved, CNMF
  4. [4] § Methods › Miniscope analysis ↔ Main/msRunCNMFE_Concat.m, lines 17–126 · score 0.67 · Gaussian kernels, noise ratio, ms, decay, peak, deconvolved

Paper

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

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The authors' code

MATLAB · 74 lines · 3.2 KB · GPL-3.0 · 1 match

  1. function runConcatStep1(path,equipment)
  5. %% Pipeline for the proper concatenation of miniscope data across sessions
  6. % Developed by Daniel Almeida Filho Mar/2020 (SilvaLab - UCLA)
  7. % If you have any questions, please send an email to
  8. % [email hidden]
  9. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  11. %% Parameters
  12. concatInfo.spatial_downsampling = 2; % (Recommended range: 2 - 4. Downsampling significantly increases computational speed, but verify it does not
  13. concatInfo.path = path;
  14. concatInfo.equipment = equipment;
  15. isnonrigid = true; % If true, performs non-rigid registration (slower). If false, rigid alignment (faster).
  16. % non-rigid is preferred within sessions.
  17. concatInfo.Sessions = dir(path);
  18. % concatInfo.Sessions = concatInfo.Sessions(3:end,:);
  19. concatInfo.Sessions = concatInfo.Sessions(3:end,:);
  21. analysis_time ='SHtemp';
  22. ConcatFolder = 'Concatenation';
  23. concatInfo.ConcatFolder = ConcatFolder;
  24. % concatInfo.order = [1 2 3]; % Order in which the files in "concatInfo.Sessions"
  25. % % will be concatenated.
  26. nSessions = size(concatInfo.Sessions,1);
  27. mkdir(strcat(path,filesep,ConcatFolder));
  28. save(strcat(path,filesep,ConcatFolder,filesep,'concatInfo.mat'),'concatInfo','-v7.3')
  30. %% Step 1: Motion correction of single sessions (NoRMCorre)
  31. Step1Dur = tic;
  32. disp('Step 1: Applying motion correction on single sessions.');
  33. plotFlag = false; %Plot the results of motion correction
  34. ROIflag = false; %Choose true if you want to select a specific ROI in the
  35. % FOV for each separate session. Pixels outside of the FOV will be deemed
  36. % zero.
  37. replaceRGBVideo = false; %Choose true if you want to replace RGB videos by their gray scale version
  38. checkMotCorr = false; %Manually check the first video of motion correction
  39. % to see if the algoirthm is capable of correcting motion properly for that specific dataset.
  40. for i = 1:nSessions
  41. cd(strcat(path,filesep,concatInfo.Sessions(i).name))
  42. ms = msGenerateVideoObjConcat(pwd, concatInfo.equipment, replaceRGBVideo, 'msCam');
  43. ms.FrameRate = round(1/(nanmedian(diff(ms.time))/1000));
  44. ms.equipment = concatInfo.equipment;
  45. if i==1
  46. concatInfo.FrameRate = ms.FrameRate;
  47. end
  48. ms.analysis_time = analysis_time;
  49. ms.ds = concatInfo.spatial_downsampling;
  50. mkdir(strcat(pwd,filesep,analysis_time));
  51. save([ms.dirName filesep 'ms.mat'],'ms');
  52. disp(['Working on Session: ' num2str(i) ' of ' num2str(nSessions)])
  53. ms = msNormCorreConcat(ms,isnonrigid,ROIflag,plotFlag,checkMotCorr);
  54. save([ms.dirName filesep 'ms.mat'],'ms');
  55. clear ms
  56. end
  58. %%% Place all the motion corrected videos in the same folder
  59. disp('Step 1.1: Copying videos to concatenate to the same folder and in the correct order.');
  60. animal={};
  61. for i = 1:nSessions
  62. actualIdx = concatInfo.order(i);
  63. cd(strcat(path,filesep,concatInfo.Sessions(actualIdx).name,filesep))
  64. load('ms.mat')
  65. animal{i}=ms;
  66. cd(analysis_time)
  67. copyfile('msvideo.avi',...
  68. strcat(path,filesep,ConcatFolder,filesep,['msvideo' num2str(i) '.avi']))
  69. clear ms
  70. end
  71. save(strcat(path,filesep,ConcatFolder,filesep,'concatInfo.mat'),'concatInfo','-v7.3')
  72. save(strcat(path,filesep,ConcatFolder,filesep,'animal.mat'),'animal','-v7.3')
  73. disp(['Total duration of Step 1 = ' num2str(toc(Step1Dur)) ' seconds.'])
  74. end

runConcatStep1.m at commit 0f96fcb, under GPL-3.0 · at the source

Overview

Authors: André F de Sousa1, Zachary E Zeidler2, Daniel G Almeida-Filho1,3, Yang Shen1,4, Alessandro Luchetti1,5, Shana Simanian1, Mouaz Mardini1, Laura A DeNardo2, Alcino J Silva1
ORCID iDs: André F de Sousa, Daniel G Almeida-Filho, Laura A DeNardo, Alcino J Silva
  1. Departments of Neurobiology, Psychiatry & Biobehavioral Sciences, and Psychology, Integrative Center for Learning and Memory, Brain Research Institute, UCLA, Los Angeles, CA USA
  2. Departments of Physiology and Neurobiology, UCLA, Los Angeles, CA USA
  3. SENAI Institute of Innovation in Advanced Health Systems, University Center SENAI, CIMATEC, Salvador, Bahia Brazil
  4. Present Address: Bioscience and Biomedical Engineering Thrust, Brain and Intelligence Research Institute, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou, China
  5. Present Address: Program in Neurosciences & Mental Health, Hospital for Sick Children, Toronto, Ontario Canada
Institutions: University of California, Los Angeles (United States); Serviço Nacional de Aprendizagem Industrial (Brazil); Universidade SENAI CIMATEC (Brazil); The Hong Kong University of Science and Technology (Guangzhou) (China); Hospital for Sick Children (Canada)
Journal: Nature neuroscience, volume 29, issue 5, pages 1191-1202
Dates: received 14 July 2024; accepted 28 January 2026; published online 28 April 2026; in print 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1038/s41593-026-02231-1 · PMID 42049880 · PMCID PMC13156042 · OpenAlex W7157212937
Open access: hybrid, a free copy (OpenAlex)
Status: code verified
Categories: mouse (organism), systems (subfield)
Methods: Connectivity, Statistics, fMRI & imaging, Single-unit activity, calcium imaging, Smoothing, state filtering, decompositions
Keywords: Hippocampus, Neural circuits
MeSH: Hippocampus*, Memory*, Prefrontal Cortex*, Animals, Entorhinal Cortex, Male, Mice, Mice, Inbred C57BL, Neural Pathways, Optogenetics (* major topic)
Topic: Memory and Neural Mechanisms (Cognitive Neuroscience, Neuroscience), according to OpenAlex
Funding: Dr. Miriam and Sheldon G. Adelson Medical Research Foundation (NA); NIA NIH HHS (R01 AG013622); U.S. Department of Health & Human Services | NIH | National Institute on Aging (R01 AG013622)
Citations: cited by 8 papers (Europe PMC); 61 references in the paper
Research resources: RRID:IMSR_JAX:007914, Fos2A-iCreER (TRAP2 RRID:IMSR_JAX:030323, RRID:IMSR_JAX:030757

Abstract

Prior memories can be integrated with novel experiences during learning to facilitate memory organization. This process must be tightly regulated to prevent inappropriate integration of unrelated memories. However, the biological mechanisms underlying such control are currently unknown. Using multiple imaging, chemogenetic and optogenetic techniques in mice, we demonstrate that the ventromedial prefrontal cortex is recruited over time to control memory integration in the hippocampus according to contextual similarities between experiences. This control is achieved through direct projections to the medial entorhinal cortex that modulate entorhinal activity, ensemble overlap in the dorsal hippocampus, memory linking, activity of neurogliaform cells in the dorsal CA1 and memory allocation. Together, our results provide new insights into the mechanisms controlling crucial processes of memory organization in the mammalian brain.

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

Repositories

Its files are read in the Code ↔ Paper reader above, with 4 matches between paragraphs and lines of code.

Zenodo 5676164

License: other-open
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: “Code availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: Image Processing Toolbox (54 files), Statistics and Machine Learning Toolbox (14 files), Signal Processing Toolbox (7 files), Parallel Computing Toolbox (6 files), Optimization Toolbox (3 files)
Availability: 1 check, the latest on 30 September 2026: the link answers (HTTP 200)
  • 30 September 2026: the link answers (HTTP 200)
275 files
At the source:

Zenodo 5676163

License: other-open
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: the references
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: Image Processing Toolbox (54 files), Statistics and Machine Learning Toolbox (14 files), Signal Processing Toolbox (7 files), Parallel Computing Toolbox (6 files), Optimization Toolbox (3 files)
Availability: 1 check, the latest on 30 September 2026: the link answers (HTTP 200)
  • 30 September 2026: the link answers (HTTP 200)
275 files
At the source:

almeida-filhodg/concatminiscope

License: GPL-3.0
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Commit: 0f96fcbdb98fd522510c8eabeee7c62e99267c87, 1 April 2022
Languages: MATLAB (272), C++ (1)
Size: 288 files, 273 scripts
Software Heritage: not archived
Found in: the Zenodo archive record
Holds: README, license file, CITATION.cff
Not found: environment file, tests, continuous integration, documentation
Tools: Image Processing Toolbox (54 files), Statistics and Machine Learning Toolbox (14 files), Signal Processing Toolbox (7 files), Parallel Computing Toolbox (6 files), Optimization Toolbox (3 files)
Availability: 1 check, the latest on 30 September 2026: the link answers
  • 30 September 2026: the link answers
275 files
At the source: github.com/Almeida-FilhoDG/ConcatMiniscope/tree/v1.0.0-beta

Code availability

Code for miniscope analysis (concat pipeline) can be found via Zenodo at 10.5281/zenodo.5676164 (ref. 53).

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:

  • 3 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 819 scripts, each with its path and the digest of its content;
  • 4 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

No dataset and no data link were found in the paper.

Data availability

All raw data reported in this study are available from the corresponding authors upon request. We chose to share raw data upon request because of the large size of all the videos and images used in our analysis. Source data are provided with this paper.

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

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, 9 authors, 2 keywords, 10 MeSH terms, 3 funders, 59 references, 3 RRIDs.

Cite

This paper

de Sousa, A. F., Zeidler, Z. E., Almeida-Filho, D. G., Shen, Y., Luchetti, A., Simanian, S., Mardini, M., DeNardo, L. A., & Silva, A. J. (2026). The prefrontal cortex controls memory organization in the hippocampus. Nature neuroscience, 29(5), 1191-1202. https://doi.org/10.1038/s41593-026-02231-1

BibTeX

@article{desousa2026prefrontal,
author = {de Sousa, André F and Zeidler, Zachary E and Almeida-Filho, Daniel G and Shen, Yang and Luchetti, Alessandro and Simanian, Shana and Mardini, Mouaz and DeNardo, Laura A and Silva, Alcino J},
title = {{The prefrontal cortex controls memory organization in the hippocampus}},
journal = {Nature neuroscience},
year = {2026},
month = apr,
volume = {29},
number = {5},
pages = {1191--1202},
publisher = {Nature Portfolio},
issn = {1097-6256},
doi = {10.1038/s41593-026-02231-1},
url = {https://doi.org/10.1038/s41593-026-02231-1},
pmid = {42049880},
pmcid = {PMC13156042}
}

RIS

TY - JOUR
AU - de Sousa, André F
AU - Zeidler, Zachary E
AU - Almeida-Filho, Daniel G
AU - Shen, Yang
AU - Luchetti, Alessandro
AU - Simanian, Shana
AU - Mardini, Mouaz
AU - DeNardo, Laura A
AU - Silva, Alcino J
TI - The prefrontal cortex controls memory organization in the hippocampus
T2 - Nature neuroscience
J2 - Nat Neurosci
PY - 2026
DA - 2026/04/28
VL - 29
IS - 5
SP - 1191
EP - 1202
SN - 1097-6256
PB - Nature Portfolio
DO - 10.1038/s41593-026-02231-1
UR - https://doi.org/10.1038/s41593-026-02231-1
LA - en
ER -

CSL-JSON

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