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191 results for “cell division”
Data Analysis for: Coupling Cell Size Regulation and Proliferation Dynamics for C. glutamicum Reveals Cell Division Based on Surface Area
<div>Data and methods of Data Analysis of: Coupling Cell Size Regulation and Proliferation Dynamics of</div> <div>C. glutamicum Reveals Cell Division Based on Surface Area</div> <div> </div> <div>Authors: Cesar Nieto and Zahra Vahdat at University of Delaware (2023)</div> <div>Correspondence: cnieto@udel.edu.</div> <div> </div> <div> </div>
Data (2) with paper "Size Laws and Division Ring Dynamics in Filamentous Escherichia coli cells"
<p>See also: https://zenodo.org/records/11401115</p> <p><strong><span>Data files related to manuscript:</span></strong></p> <p><span>Wehrens M, Ershov D, Rozendaal R, Walker N, Schultz D, Kishony R, Levin PA, Tans SJ (2018). “Size Laws and Division Ring Dynamics in Filamentous Escherichia coli cells”. Current Biology. </span></p> <p><span><a href="https://doi.org/10.1016/j.cub.2018.02.006">https://doi.org/10.1016/j.cub.2018.02.006</a></span></p> <p><strong><span> </span></strong></p> <p><strong><span>Scripts are available at:</span></strong></p> <p><a href="https://github.com/TansLab/Tans_filamentation"><span>https://github.com/TansLab/Tans_filamentation</span></a></p> <p><span> </span></p> <p><span>And you will also need the additional scripts from the repositories:</span></p> <p><a href="https://github.com/TansLab/Common_libraries"><span>https://github.com/TansLab/Common_libraries</span></a></p> <p><a href="https://github.com/TansLab/Tans_Schnitzcells"><span>https://github.com/TansLab/Tans_Schnitzcells</span></a></p> <p><span> </span></p> <p><strong><span>Script that generates figures:</span></strong></p> <p><a href="https://github.com/TansLab/Tans_filamentation/blob/master/ershovwehrensallfigures.m"><span>https://github.com/TansLab/Tans_filamentation/blob/master/ershovwehrensallfigures.m</span></a></p> <p><span> </span></p> <p><em><span>And more specifically, data is loaded, (partially analyzed,) and plotted here:</span></em></p> <p><a href="https://github.com/TansLab/Tans_filamentation/blob/master/script20160429_filamentRecoveryDivisionRatioss.m"><span>https://github.com/TansLab/Tans_filamentation/blob/master/script20160429_filamentRecoveryDivisionRatioss.m</span></a></p> <p> </p> <p><strong><span>Figure 3</span></strong></p> <p><strong><span> </span></strong></p> <p><strong><span>See also</span></strong></p> <p><span><a href="https://github.com/TansLab/Tans_filamentation/blob/master/ershovwehrensallfigures.m">https://github.com/TansLab/Tans_filamentation/blob/master/ershovwehrensallfigures.m</a></span></p> <p><span><a href="https://github.com/TansLab/Tans_filamentation/blob/master/script20160422_filamentRecoveryFtslabelLocations.m">https://github.com/TansLab/Tans_filamentation/blob/master/script20160422_filamentRecoveryFtslabelLocations.m</a></span></p> <p><span> </span></p> <p><span>Related files:</span></p> <table> <tbody> <tr> <td> <p><strong><span>Data files for cell morphology properties</span></strong></p> </td> </tr> <tr> <td> <p><span>2016-04-07_FilaRecovery_asc777/pos2crop/data/pos2crop-skeletonData.mat</span></p> </td> </tr> <tr> <td> <p><span>2016-04-07_FilaRecovery_asc777/pos3crop/data/pos3crop-skeletonData.mat</span></p> </td> </tr> </tbody> </table> <p><span> </span></p> <table> <tbody> <tr> <td> <p><strong><span>Data files with fluorescence data</span></strong></p> </td> </tr> <tr> <td> <p><span>2016-04-07_FilaRecovery_asc777/pos2crop/analysis/straightenedCells/2016-04-07pos2crop_straightFluorData.mat</span></p> </td> </tr> <tr> <td> <p><span>2016-04-07_FilaRecovery_asc777/pos3crop/analysis/straightenedCells/2016-04-07pos3crop_straightFluorData.mat</span></p> </td> </tr> </tbody> </table> <p><span> </span></p> <table> <tbody> <tr> <td> <p><strong><span>Data files with division and lineage data (also supplied above)</span></strong></p> </td> </tr> <tr> <td> <p><span>2016-04-07_FilaRecovery_asc777/pos2crop/data/pos2crop-Schnitz.mat</span></p> </td> </tr> <tr> <td> <p><span>2016-04-07_FilaRecovery_asc777/pos3crop/data/pos3crop-Schnitz.mat</span></p> </td> </tr> </tbody> </table> <p><span> </span></p> <p><strong><span>Supplemental figure with nucleoid data</span></strong></p> <p><strong><span> </span></strong></p> <p><strong><span>See also</span></strong></p> <p><span><a href="https://github.com/TansLab/Tans_filamentation/blob/master/ershovwehrensallfigures.m">https://github.com/TansLab/Tans_filamentation/blob/master/ershovwehrensallfigures.m</a></span></p> <p><span><a href="https://github.com/TansLab/Tans_filamentation/blob/master/script20160422_filamentRecoveryFtslabelLocations.m">https://github.com/TansLab/Tans_filamentation/blob/master/script20160422_filamentRecoveryFtslabelLocations.m</a></span></p> <p><strong><span> </span></strong></p> <p><span>Related files:<br></span></p> <table> <tbody> <tr> <td> <p><strong><span>Data files for cell morphology properties</span></strong></p> </td> </tr> <tr> <td> <p><span>2017-11-08_FilaRecovery_asc1106_hupA-mCherry/pos1cropd/data/pos1cropd-skeletonData.mat</span></p> </td> </tr> <tr> <td> <p><span>2017-10-12_FilaRecovery_hupA-mRuby2/pos1cropa2/data/pos1cropa2-skeletonData.mat</span></p> </td> </tr> </tbody> </table> <p><span> </span></p> <table> <tbody> <tr> <td> <p><strong><span>Data files with fluorescence data</span></strong></p> </td> </tr> <tr> <td> <p><span>2017-11-08_FilaRecovery_asc1106_hupA-mCherry/pos1cropd/analysis/straightenedCells/2017-11-08pos1cropd_straightFluorData.mat</span></p> </td> </tr> <tr> <td> <p><span>2017-10-12_FilaRecovery_hupA-mRuby2/pos1cropa2/analysis/straightenedCells/2017-10-12pos1cropa2_straightFluorData.mat</span></p> </td> </tr> </tbody> </table> <p><span> </span></p> <table> <tbody> <tr> <td> <p><strong><span>Data files with division and lineage data (also supplied above)</span></strong></p> </td> </tr> <tr> <td> <p><span>2017-11-08_FilaRecovery_asc1106_hupA-mCherry/pos1cropd/data/pos1cropd-Schnitz.mat</span></p> </td> </tr> <tr> <td> <p><span>2017-10-12_FilaRecovery_hupA-mRuby2/pos1cropa2/data/pos1cropa2-Schnitz.mat</span></p> </td> </tr> </tbody> </table> <p><span> </span></p> <p><span>Lookup data file: 2017-11-08_FilaRecovery_asc1106_hupA-mCherry/pos1cropd/data/slookup.mat</span></p>
Data with paper "Size Laws and Division Ring Dynamics in Filamentous Escherichia coli cells"
<p>See also the other Zenodo record: https://zenodo.org/records/11401470</p> <p> </p> <p><strong>Data files related to manuscript:</strong></p> <p>Wehrens M, Ershov D, Rozendaal R, Walker N, Schultz D, Kishony R, Levin PA, Tans SJ (2018). “Size Laws and Division Ring Dynamics in Filamentous Escherichia coli cells”. Current Biology.</p> <p><a href="https://doi.org/10.1016/j.cub.2018.02.006">https://doi.org/10.1016/j.cub.2018.02.006</a></p> <p> </p> <p>Currently, single cell experimental time trace data for figures 1, 2 and 4 is added. Additional data will follow.</p> <p><strong> </strong></p> <p><strong>Scripts are available at:</strong></p> <p><a href="https://github.com/TansLab/Tans_filamentation">https://github.com/TansLab/Tans_filamentation</a></p> <p> </p> <p>And you will also need the additional scripts from the repositories:</p> <p><a href="https://github.com/TansLab/Common_libraries">https://github.com/TansLab/Common_libraries</a></p> <p><a href="https://github.com/TansLab/Tans_Schnitzcells">https://github.com/TansLab/Tans_Schnitzcells</a></p> <p> </p> <p><strong>Script that generates figures:</strong></p> <p><a href="https://github.com/TansLab/Tans_filamentation/blob/master/ershovwehrensallfigures.m">https://github.com/TansLab/Tans_filamentation/blob/master/ershovwehrensallfigures.m</a></p> <p> </p> <p><em>And more specifically, data is loaded, (partially analyzed,) and plotted here:</em></p> <p><a href="https://github.com/TansLab/Tans_filamentation/blob/master/script20160429_filamentRecoveryDivisionRatioss.m">https://github.com/TansLab/Tans_filamentation/blob/master/script20160429_filamentRecoveryDivisionRatioss.m</a></p> <p> </p> <p><strong>Description of the .mat files</strong></p> <p> </p> <p>These .mat files contain the lineage information, which were used to generate figures 1 and 2.</p> <p> </p> <p>Each row corresponds to a cell from birth to division.</p> <p> </p> <p>Most important fields are:</p> <p>P is its parent cell (number referring to the row of the table).</p> <p>E is the daughter cell after this cell divides</p> <p>D is the other daughter cell after this cell divides</p> <p>frame_nrs is in which frame this cell lived</p> <p>areapx is its area in pixels</p> <p> </p> <p>Different methods were used to determine the bacterias length. For the tetracycline experiments, often the field “length_fitNew” was used, which is a higher order polynomial fitted through the bacterium. For the other stress conditions, mostly the field “length_skeleton” was used, which is the length of the skeleton of the bacteria, extrapolated until it reaches the bacterial edge (this was done because in those experiments, these bacteria often had weird shapes that couldn’t be fitted by polynomials).</p> <p> </p> <p>The growth rate of the bacteria is determined by fitting an exponential curve through length information of multiple frames. Given the fluctuation of growth rates, sometimes bacteria grow relatively slow over a certain amount of frames, or relatively fast. Therefor, sometimes the fit is done using more or less frames. The growth rate information can be found in e.g. the parameters 'muP15_fitNew_all','muP9_skeleton_all','muP5_skeleton_all', where mu refers to growth rate, PX indicates X frames around the frame of interest were used for the fit, and fitNew_all or skeleton_all refers respectively to which length parameter was used for the fit.</p> <p> </p> <p>Note that birth sizes and interdivision times, as wel as added length, can be calculated from the above parameters using the data structure. (See also applicable scripts.)</p> <p> </p> <p>The data also contains more fields with information about length and size, and also fields for fluorescence data. The latter is not really applicable here. </p> <p> </p> <p>See also the methods section of the paper for more information.</p> <p> </p> <p><strong>INFORMATION ABOUT THE DATA</strong></p> <p> </p> <p><strong>Files for the SulA condition:</strong></p> <table> <tbody> <tr> <td> <p><strong>Data file</strong></p> </td> <td> <p><strong>Switch time from stress to stress-free condition (min)</strong></p> </td> </tr> <tr> <td> <p>\2016-04-08_FilaRecovery_sulA_recovery_200uM_IPTG\pos1crop\data\pos1crop-Schnitz.mat</p> </td> <td> <p>0</p> </td> </tr> <tr> <td> <p>\2016-04-08_FilaRecovery_sulA_recovery_200uM_IPTG\pos2crop\data\pos2crop-Schnitz.mat</p> </td> <td> <p>0</p> </td> </tr> <tr> <td> <p>\2016-04-08_FilaRecovery_sulA_recovery_200uM_IPTG\pos3crop\data\pos3crop-Schnitz.mat</p> </td> <td> <p>0</p> </td> </tr> <tr> <td> <p>\2016-04-08_FilaRecovery_sulA_recovery_200uM_IPTG\pos4crop\data\pos4crop-Schnitz.mat</p> </td> <td> <p>0</p> </td> </tr> <tr> <td> <p>\2016-04-08_FilaRecovery_sulA_recovery_200uM_IPTG\pos7crop\data\pos7crop-Schnitz.mat</p> </td> <td> <p>0</p> </td> </tr> </tbody> </table> <p><em>If switch time is zero, recording started at the switch time.</em></p> <p> </p> <p><strong>For the temperature condition</strong></p> <table> <tbody> <tr> <td> <p><strong>Data file</strong></p> </td> <td> <p><strong>Switch time from stress to stress-free condition (min)</strong></p> </td> </tr> <tr> <td> <p>2016-03-23_FilaRecovery_asc777_42C\pos4crop\data\pos4crop-Schnitz.mat</p> </td> <td> <p>450</p> </td> </tr> <tr> <td> <p>2016-04-07_FilaRecovery_asc777\pos2crop\data\pos2crop-Schnitz.mat</p> </td> <td> <p>329</p> </td> </tr> </tbody> </table> <p> </p> <p><strong>Delta min tetracycline condition</strong></p> <table> <tbody> <tr> <td> <p><strong>Data file</strong></p> </td> <td> <p><strong>Switch time from stress to stress-free condition (min)</strong></p> </td> </tr> <tr> <td> <p>2017-09-22_FilaRecovery_asc1035_DeltaMinCDE\pos1cropb\data\pos1cropb-Schnitz.mat</p> </td> <td> <p>5</p> </td> </tr> <tr> <td> <p>2017-09-22_FilaRecovery_asc1035_DeltaMinCDE\pos2cropa\data\pos2cropa-Schnitz.mat</p> </td> <td> <p>5</p> </td> </tr> <tr> <td> <p>2017-09-22_FilaRecovery_asc1035_DeltaMinCDE\pos2cropb\data\pos2cropb-Schnitz.mat</p> </td> <td> <p>5</p> </td> </tr> <tr> <td> <p>2017-09-22_FilaRecovery_asc1035_DeltaMinCDE\pos2cropc\data\pos2cropc-Schnitz.mat</p> </td> <td> <p>5</p> </td> </tr> <tr> <td> <p>2017-09-22_FilaRecovery_asc1035_DeltaMinCDE\pos3cropa\data\pos3cropa-Schnitz.mat</p> </td> <td> <p>5</p> </td> </tr> </tbody> </table> <p> </p> <p><strong>Tetracycline data</strong></p> <p><em>Only data sets 1 to 5 where used here</em></p> <p> </p> <table> <tbody> <tr> <td> <p><strong>Data file</strong></p> </td> <td> <p><strong>Switch time from stress to stress-free condition (min)</strong></p> </td> </tr> <tr> <td> <p>F schijf AmolfBackup_3april2014\USE_DIV\1uM_pos3_long.mat</p> </td> <td> <p>890.9800 </p> </td> </tr> <tr> <td> <p>F schijf AmolfBackup_3april2014\USE_DIV\1uM_pos4.mat</p> </td> <td> <p>404.7500 </p> </td> </tr> <tr> <td> <p>F schijf AmolfBackup_3april2014\USE_DIV\1uM_pos4_long.mat</p> </td> <td> <p>0 </p> </td> </tr> <tr> <td> <p>F schijf AmolfBackup_3april2014\USE_DIV\1uM_pos5.mat</p> </td> <td> <p>529.7600 </p> </td> </tr> <tr> <td> <p>F schijf AmolfBackup_3april2014\USE_DIV\1uM_pos5_long.mat</p> </td> <td> <p>0</p> </td> </tr> <tr> <td> <p>F schijf AmolfBackup_3april2014\USE_DIV\2uM_pos2.mat</p> </td> <td> <p>NA</p> </td> </tr> <tr> <td> <p>F schijf AmolfBackup_3april2014\USE_DIV\2uM_pos4.mat</p> </td> <td> <p>NA</p> </td> </tr> <tr> <td> <p>F schijf AmolfBackup_3april2014\USE_DIV\2uM_pos6.mat</p> </td> <td> <p>NA</p> </td> </tr> <tr> <td> <p>F schijf AmolfBackup_3april2014\USE_DIV\10uM_pos1.mat</p> </td> <td> <p>NA</p> </td> </tr> <tr> <td> <p>F schijf AmolfBackup_3april2014\USE_DIV\10uM_pos3.mat</p> </td> <td> <p>NA</p> </td> </tr> <tr> <td> <p>F schijf AmolfBackup_3april2014\USE_DIV\10uM_pos6_long.mat</p> </td> <td> <p>NA</p> </td> </tr> </tbody> </table> <p> </p> <p><strong>Tetracycline data 2 (redundant with above)</strong></p> <p> </p> <table> <tbody> <tr> <td> <p><strong>Data file</strong></p> </td> <td> <p><strong>Switch time from stress to stress-free condition (min)</strong></p> </td> </tr> <tr> <td> <p>2013-12-09\pos3crop\data\pos3crop-Schnitz.mat</p> </td> <td> <p>890.9800 </p> </td> </tr> <tr> <td> <p>2013-09-24\pos4crop\data\pos4crop-Schnitz.mat</p> </td> <td> <p>404.7500 </p> </td> </tr> <tr> <td> <p>2013-12-16\pos4crop\data\pos4crop-Schnitz.mat</p> </td> <td> <p>0 </p> </td> </tr> <tr> <td> <p>2013-09-24\pos5crop\data\pos5crop-Schnitz.mat</p> </td> <td> <p>529.7600 </p> </td> </tr> <tr> <td> <p>2013-12-16\pos5crop\data\pos5crop-Schnitz.mat</p> </td> <td> <p>0</p> </td> </tr> </tbody> </table> <p> </p> <p> </p>
SASDM95 – Candida albicans Ras-like protein 1 in complex with the guanine nucleotide exchange factor region of cell division control protein 25
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SASDM85 – GTP-binding domain of Candida albicans Ras-like protein 1 in complex with the guanine nucleotide exchange factor region of cell division control protein 25
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SASDM75 – Ras-like protein 1 guanine nucleotide exchange factor region of Candida albicans cell division control protein 25
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Deep learning for rapid analysis of cell divisions in vivo during epithelial morphogenesis and repair
<div> <p>Database for paper:</p> <p><a href="https://doi.org/10.7554/eLife.87949.2">doi.org/10.7554/eLife.87949.2</a></p> <p>The scripts for using our deep learning algrithm to detect cell divisions via a napari plugin can be found here:</p> <p>https://github.com/turleyjm/cell-division-dl-plugin</p> <p>The notebooks and analysis for training and evaluating the model are also given in this repository.</p> </div>
Data and code for "Migration and division in cell monolayers on substrates with topological defects"
<p>Raw data for experiment (experiment.zip) and basic simulation code (simulation.zip) for the paper "Migration and division in cell monolayers on substrates with topological defects"</p>
A novel pattern of germ cell divisions in the production of Hymenopteran insect eggs
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Data from: Division of functional roles for termite gut protists revealed by single-cell transcriptomes
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Host glutathione is required for Rickettsia parkeri cell division and intracellular survival
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Unique mode of cell division by the mycobacterial genetic resister clones emerging de novo from the antibiotic surviving population
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Data from: Widespread dysregulation of long non-coding genes associated with fatty acid metabolism, cell division, and immune response gene networks in xenobiotic-exposed rat liver
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Data from: Drosophila Sulf1 is required for the termination of intestinal stem cell division during regeneration
Stem cell division is activated to trigger regeneration in response to tissue damage. The molecular mechanisms by which this stem cell mitotic activity is properly repressed at the end of regeneration are poorly understood. Here, we show that a specific modification of heparan sulfate is crucial for regulating Drosophila intestinal stem cell (ISC) division during normal midgut homeostasis and regeneration. Loss of the extracellular heparan sulfate endosulfatase Sulf1 resulted in increased ISC division during normal homeostasis, which was caused by upregulation of mitogenic signaling including the JAK-STAT, EGFR and Hedgehog pathways. Using a regeneration model, we found that ISCs failed to properly halt division at the termination stage in Sulf1 mutants, showing that Sulf1 is required for terminating ISC division at the end of regeneration. We propose that post-transcriptional regulation of mitogen signaling by heparan sulfate structural modifications provides a new regulatory step for precise temporal control of stem cell activity during regeneration.
Transcriptional activation of Arabidopsis zygotes is required for initial cell divisions
<p>Commonly referred to as the maternal-to-zygotic transition, the shift of developmental control from maternal-to-zygotic genomes is a key event during animal and plant embryogenesis. Together with the degradation of parental gene products, the increased transcriptional activities of the zygotic genome remodels the early embryonic transcriptome during this transition. Although evidence from multiple flowering plants suggests that zygotes become transcriptionally active soon after fertilization, the timing and developmental requirements of zygotic genome activation in Arabidopsis thaliana (Arabidopsis) remained a matter of debate until recently. In this report, we optimized an expansion microscopy technique for robust immunostaining of Arabidopsis ovules and seeds. This enabled the detection of marks indicative of active transcription in zygotes before the first cell division. Moreover, we employed a live-imaging culture system together with transcriptional inhibitors to demonstrate that such active transcription is physiologically required in zygotes and early embryos. Our results indicate that zygotic genome activation occurs soon after fertilization and is required for the initial zygotic divisions in Arabidopsis.</p>
Fig. 1 in Effects of Roscovitine on Schedule of Divisional Morphogenesis, Basal Bodies Proliferation and Cell Divisions in Tetrahymena thermophila
Fig. 1. Divisional morphogenesis and cytokinesis in untreated (control) T. thermophila. Cells were immunostained with the anti-centrin 20H5 antibody. A–F' stomatogenesis, stages I–VI; G–H cytokinesis. AF – an anarchic field, ARF – parental apical ring of filaments, mARF material for new ARF localised on in the proximal ends (couplets of BBs) of cortical rows in opisthe cell, FZ – fission zone, OA1 and OA2 – parental and new oral apparatuses, OC – parental oral crescent, nOC – new oral crescents in both daughter cells. Bar: 10 µm for A–H.
Fig. 11 in Effects of Roscovitine on Schedule of Divisional Morphogenesis, Basal Bodies Proliferation and Cell Divisions in Tetrahymena thermophila
Fig. 11. Cortical structures of T. thermophila immunogoldlabelled with anti-cdc14A antibody. A – longitudinal section of the ciliated basal body; B – transversal section of the fragment of the cortical row; C – section at the level of basal bodies of oral membranelle. Kt – kinetodesmal fiber, pc – postciliary microtubules, arrowhead – filamentous material. Bar: 1 μm.
Fig. 3 in Effects of Roscovitine on Schedule of Divisional Morphogenesis, Basal Bodies Proliferation and Cell Divisions in Tetrahymena thermophila
Fig. 3. Divisional morphogenesis and cytokinesis in T. thermophila after 5.5 h treatment with roscovitine. Cells were immunostained with the anti-centrin 20H5 antibody. A–C – stage VI of divisional morphogenesis; D–F' – cytokinesis; A and A' – ventral and dorsal views of the same cell. Other explanations as in Fig. 1. Bar in F': 10 µm for A–F'.
Menin Associates with the Mitotic Spindle and is Important for Cell Division
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Data from: Drosophila Sulf1 is required for the termination of intestinal stem cell division during regeneration
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.