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Blot force 6, blot time 3 s, drain time 1s."},{"descriptionType":"Other","description":"Pseudomonas_JT2944Tilt408.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.4 GB\n\nPseudomonas_JT2944Tilt408_full.rec,  Reconstruction (Pixel Size 1.56 nm), 444.5 MB"}],"geoLocations":[],"fundingReferences":[{"funderName":"NIH"},{"funderName":"HHMI"},{"funderName":"Beckman Institute"},{"funderIdentifierType":"ROR","funderName":"Gordon and Betty Moore Foundation","funderIdentifier":"006wxqw41"},{"funderIdentifierType":"ROR","funderName":"Agouron Institute","funderIdentifier":"05vmwhp17"},{"funderIdentifierType":"ROR","funderName":"John Templeton Foundation","funderIdentifier":"035tnyy05"}],"url":"https://data.caltech.edu/doi/10.22002/e9ky3-f9z92","contentUrl":null,"metadataVersion":2,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"api","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2023-06-09T16:26:01Z","registered":"2023-06-09T16:26:01Z","published":null,"updated":"2026-06-26T22:57:15Z"},"relationships":{"client":{"data":{"id":"caltech.data","type":"clients"}}}},{"id":"10.22002/rh9b6-0b465","type":"dois","attributes":{"doi":"10.22002/rh9b6-0b465","identifiers":[{"identifier":"oai:data.caltech.edu:rh9b6-0b465","identifierType":"oai"},{"identifier":"mka2019-11-19-168","identifierType":"tiltid"}],"creators":[{"nameType":"Personal","affiliation":["California Institute of Technology"],"givenName":"Mohammed","familyName":"Kaplan","name":"Kaplan, Mohammed","nameIdentifiers":[]}],"titles":[{"title":"Hpylori_dfliQ"}],"publisher":"CaltechDATA","container":{},"publicationYear":2019,"subjects":[{"subject":"Helicobacter pylori"},{"subject":"26695"},{"subject":"Single Axis"},{"subject":"Caltech Titan Krios"},{"subject":"Serial EM"},{"subject":"pipeline"},{"subject":"Raptor"}],"contributors":[],"dates":[{"date":"2019","dateType":"Issued"},{"date":"2019-11-19","dateType":"Collected"},{"date":"2019-12-09","dateType":"Created"},{"date":"2019-12-12","dateType":"Updated"}],"language":"en","types":{"schemaOrg":"Dataset","resourceTypeGeneral":"Dataset","citeproc":"dataset","bibtex":"misc","ris":"DATA","resourceType":""},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":["jpg","mp4","rec","mrc"],"version":null,"rightsList":[{"rightsIdentifierScheme":"SPDX","rightsUri":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rights":"Creative Commons Attribution Non Commercial 4.0 International","rightsIdentifier":"cc-by-nc-4.0"}],"descriptions":[{"descriptionType":"Abstract","description":"These are fast tilt series taken on the Krios for dFliM mutant of Helicobacter  .  pylori."},{"descriptionType":"TechnicalInfo","description":"Tilt Series Date: 2019-11-19\nData Taken By: Mohammed Kaplan\nSpecies / Specimen: Helicobacter pylori\nStrain: 26695\nTilt Series Settings:  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 120.0 eV/Ų,  defocus: -6.0 μm,  magnification: 19500x. \nMicroscope: Caltech Titan Krios\nAcquisition Software: Serial EM\nUpload Method: pipeline\nProcessing Software Used: Raptor\nCollaborators and Roles: I received these cells from Carrie Schaffer from the university of Kentucky. These are wild type cells but they don't express complete FliP protein. Therefore, they don't . assemble full flagella. We knocked out FliQ protein of the flagellar motor to study the early assembly states of flagellar motor.\nPurification / Growth Conditions / Treatment: I grew the cells on blood agar plates from -80 stock at 37C with 5% CO2. The cells were grown for 48 hours and then spread on a new plate with a cotton swab and left to grow for 24 hours. . The grids . were prepared from both batches (48 hours, and 24 hours, separately).\nSample Preparation: The samples were prepared with Vitrobot IV. Blotting conditions were either: blot force 6, blot, time 3, drain time 1 OR blot force -3, blot time 4, drain time 1, 100% humidity. Cu grids. . 10 nm gold."},{"descriptionType":"Other","description":"Hpylori_dfliQ_168_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 1.9 GB\n\nHpylori_dfliQ_168_af_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB"}],"geoLocations":[],"fundingReferences":[{"funderName":"NIH"},{"funderName":"HHMI"},{"funderName":"Beckman Institute"},{"funderIdentifierType":"ROR","funderName":"Gordon and Betty Moore Foundation","funderIdentifier":"006wxqw41"},{"funderIdentifierType":"ROR","funderName":"Agouron Institute","funderIdentifier":"05vmwhp17"},{"funderIdentifierType":"ROR","funderName":"John Templeton Foundation","funderIdentifier":"035tnyy05"}],"url":"https://data.caltech.edu/doi/10.22002/rh9b6-0b465","contentUrl":null,"metadataVersion":2,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"api","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2023-06-09T16:26:16Z","registered":"2023-06-09T16:26:16Z","published":null,"updated":"2026-06-26T22:57:12Z"},"relationships":{"client":{"data":{"id":"caltech.data","type":"clients"}}}},{"id":"10.22002/79hej-4k407","type":"dois","attributes":{"doi":"10.22002/79hej-4k407","identifiers":[{"identifier":"oai:data.caltech.edu:79hej-4k407","identifierType":"oai"},{"identifier":"mka2019-11-24-75","identifierType":"tiltid"}],"creators":[{"nameType":"Personal","affiliation":["California Institute of Technology"],"givenName":"Mohammed","familyName":"Kaplan","name":"Kaplan, Mohammed","nameIdentifiers":[]}],"titles":[{"title":"Hpylori_dFliM"}],"publisher":"CaltechDATA","container":{},"publicationYear":2019,"subjects":[{"subject":"Helicobacter pylori"},{"subject":"26695"},{"subject":"Single Axis"},{"subject":"Caltech Titan Krios"},{"subject":"Serial EM"},{"subject":"pipeline"},{"subject":"Raptor"}],"contributors":[],"dates":[{"date":"2019","dateType":"Issued"},{"date":"2019-11-24","dateType":"Collected"},{"date":"2019-12-23","dateType":"Created"},{"date":"2020-01-06","dateType":"Updated"}],"language":"en","types":{"schemaOrg":"Dataset","resourceTypeGeneral":"Dataset","citeproc":"dataset","bibtex":"misc","ris":"DATA","resourceType":""},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":["jpg","mp4","rec","mrc"],"version":null,"rightsList":[{"rightsIdentifierScheme":"SPDX","rightsUri":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rights":"Creative Commons Attribution Non Commercial 4.0 International","rightsIdentifier":"cc-by-nc-4.0"}],"descriptions":[{"descriptionType":"Abstract","description":"These are fast tilt series that I collected on Hpylori_dFliM (dFliP also) on the Titan Krios."},{"descriptionType":"TechnicalInfo","description":"Tilt Series Date: 2019-11-24\nData Taken By: Mohammed Kaplan\nSpecies / Specimen: Helicobacter pylori\nStrain: 26695\nTilt Series Settings:  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 120.0 eV/Ų,  defocus: -8.0 μm,  magnification: 19500x. \nMicroscope: Caltech Titan Krios\nAcquisition Software: Serial EM\nUpload Method: pipeline\nProcessing Software Used: Raptor\nCollaborators and Roles: I received these cells from Carrie Schaffer from the university of Kentucky. These are wild type cells but they don't express complete FliP . protein. Therefore, they don't assemble full flagella. We knocked out FliM protein of the flagellar motor to study the early assembly states of . flagellar motor.\nPurification / Growth Conditions / Treatment: I grew the cells on blood agar plates from -80 stock at 37C with 5% CO2. the cells were grown for 48 hours and then spread on a new plate with a cotton swab and left to . grow for 24 hours. The grids were prepared from both batches (48 hours, and 24 hours, separately).\nSample Preparation: The samples were prepared with Vitrobot IV. Blotting conditions were either: blot force 6, blot time 3, drain time 1 OR blot force -3, blot time 4, drain time 1, 100% . humidity. Cu grids. 10 nm gold."},{"descriptionType":"Other","description":"Hpylori_dfliM_084_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 1.9 GB\n\nHpylori_dfliM_084_af_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB"}],"geoLocations":[],"fundingReferences":[{"funderName":"NIH"},{"funderName":"HHMI"},{"funderName":"Beckman Institute"},{"funderIdentifierType":"ROR","funderName":"Gordon and Betty Moore Foundation","funderIdentifier":"006wxqw41"},{"funderIdentifierType":"ROR","funderName":"Agouron Institute","funderIdentifier":"05vmwhp17"},{"funderIdentifierType":"ROR","funderName":"John Templeton Foundation","funderIdentifier":"035tnyy05"}],"url":"https://data.caltech.edu/doi/10.22002/79hej-4k407","contentUrl":null,"metadataVersion":2,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"api","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2023-06-09T16:26:29Z","registered":"2023-06-09T16:26:30Z","published":null,"updated":"2026-06-26T22:57:10Z"},"relationships":{"client":{"data":{"id":"caltech.data","type":"clients"}}}},{"id":"10.22002/znra5-cxy84","type":"dois","attributes":{"doi":"10.22002/znra5-cxy84","identifiers":[{"identifier":"oai:data.caltech.edu:znra5-cxy84","identifierType":"oai"},{"identifier":"mka2020-02-09-23","identifierType":"tiltid"}],"creators":[{"nameType":"Personal","affiliation":["California Institute of Technology"],"givenName":"Mohammed","familyName":"Kaplan","name":"Kaplan, Mohammed","nameIdentifiers":[]}],"titles":[{"title":"Ecoli_EPEC_8612"}],"publisher":"CaltechDATA","container":{},"publicationYear":2020,"subjects":[{"subject":"Escherichia coli"},{"subject":"8612, EPEC Δrof1-escLΔrof3-mpcΔescN-espFΔflhBAΔfliOPQRΔminCD"},{"subject":"Single Axis"},{"subject":"Caltech Titan Krios"},{"subject":"Serial EM"},{"subject":"pipeline"},{"subject":"None"}],"contributors":[],"dates":[{"date":"2020","dateType":"Issued"},{"date":"2020-02-09","dateType":"Collected"},{"date":"2020-02-10","dateType":"Created"},{"date":"2022-10-05","dateType":"Updated"}],"language":"en","types":{"schemaOrg":"Dataset","resourceTypeGeneral":"Dataset","citeproc":"dataset","bibtex":"misc","ris":"DATA","resourceType":""},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":["mrc","mdoc","jpg"],"version":null,"rightsList":[{"rightsIdentifierScheme":"SPDX","rightsUri":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rights":"Creative Commons Attribution Non Commercial 4.0 International","rightsIdentifier":"cc-by-nc-4.0"}],"descriptions":[{"descriptionType":"Abstract","description":"These are E coli cells (EPEC 8612) obtained from Ritesh (Ilan Rosenshine lab at the Hebrew  .  university). The idea is to image bacterial nanotubes in these cells."},{"descriptionType":"TechnicalInfo","description":"Tilt Series Date: 2020-02-09\nData Taken By: Mohammed Kaplan\nSpecies / Specimen: Escherichia coli\nStrain: 8612, EPEC Δrof1-escLΔrof3-mpcΔescN-espFΔflhBAΔfliOPQRΔminCD\nTilt Series Settings:  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 120.0 eV/Ų,  defocus: -8.0 μm,  magnification: 19500x. \nMicroscope: Caltech Titan Krios\nAcquisition Software: Serial EM\nUpload Method: pipeline\nProcessing Software Used: None\nCollaborators and Roles: These cells were prepared with Ritesh in Ilan Rosenshine lab at the Hebrew University.\nPurification / Growth Conditions / Treatment: The cells were incubated on grids on agar plates (DMEM agar plates for three hours) and then . on starvation medium agar plate for 1 hour Then washed with PBS and blotted and then plunge . frozen. Yuxi helped in sample preparation and data collection\nSample Preparation: The cells were incubated on grids on agar plates (DMEM agar plates for three hours) and then . on starvation medium agar plate for 1 hour"},{"descriptionType":"Other","description":"EPEC_8612_tilt55.mrc,  Tilt Series (Pixel Size 0.449 nm), 480.6 MB\n\nEPEC_8612_tilt55.mrc.mdoc,  8.6 kB"}],"geoLocations":[],"fundingReferences":[{"funderName":"NIH"},{"funderName":"HHMI"},{"funderName":"Beckman Institute"},{"funderIdentifierType":"ROR","funderName":"Gordon and Betty Moore Foundation","funderIdentifier":"006wxqw41"},{"funderIdentifierType":"ROR","funderName":"Agouron Institute","funderIdentifier":"05vmwhp17"},{"funderIdentifierType":"ROR","funderName":"John Templeton Foundation","funderIdentifier":"035tnyy05"}],"url":"https://data.caltech.edu/doi/10.22002/znra5-cxy84","contentUrl":null,"metadataVersion":2,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"api","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2023-06-09T16:27:13Z","registered":"2023-06-09T16:27:13Z","published":null,"updated":"2026-06-26T22:57:04Z"},"relationships":{"client":{"data":{"id":"caltech.data","type":"clients"}}}},{"id":"10.22002/gyq44-bq059","type":"dois","attributes":{"doi":"10.22002/gyq44-bq059","identifiers":[{"identifier":"oai:data.caltech.edu:gyq44-bq059","identifierType":"oai"},{"identifier":"lma2018-09-14-8","identifierType":"tiltid"}],"creators":[{"nameType":"Personal","affiliation":["California Institute of Technology"],"givenName":"LaurenAnn","familyName":"Metskas","name":"Metskas, LaurenAnn","nameIdentifiers":[]}],"titles":[{"title":"Shewanella OMV delMTR delDMSOR"}],"publisher":"CaltechDATA","container":{},"publicationYear":2018,"subjects":[{"subject":"Shewanella oneidensis"},{"subject":"MR-1"},{"subject":"Single Axis"},{"subject":"Serial EM"},{"subject":"rundir"},{"subject":"IMOD"},{"subject":"ctffind4"},{"subject":"custom scripts"}],"contributors":[],"dates":[{"date":"2018","dateType":"Issued"},{"date":"2018-09-14","dateType":"Collected"},{"date":"2019-05-23","dateType":"Created"},{"date":"2019-05-23","dateType":"Updated"}],"language":"en","types":{"schemaOrg":"Dataset","resourceTypeGeneral":"Dataset","citeproc":"dataset","bibtex":"misc","ris":"DATA","resourceType":""},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":["mdoc","st","rec","bz2","jpg","mp4"],"version":null,"rightsList":[{"rightsIdentifierScheme":"SPDX","rightsUri":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rights":"Creative Commons Attribution Non Commercial 4.0 International","rightsIdentifier":"cc-by-nc-4.0"}],"descriptions":[{"descriptionType":"Abstract","description":"Shewanella outer membrane vesicles, delMTR, del DMSO Reductase, high resolution"},{"descriptionType":"TechnicalInfo","description":"Tilt Series Date: 2018-09-14\nData Taken By: LaurenAnn Metskas\nSpecies / Specimen: Shewanella oneidensis\nStrain: MR-1\nTilt Series Settings:  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 120.0 eV/Ų,  defocus: 0.0 μm,  magnification: 82000x. \nAcquisition Software: Serial EM\nUpload Method: rundir\nProcessing Software Used: IMOD, ctffind4, custom scripts\nCollaborators and Roles: purified by Lori Zacharoff in the El Naggar lab at USC; data collected by Lauren Ann Metskas; data processed by Lauren Ann Metskas\nSample Preparation: protochip c-flat 2/2-300 grid, 10nm BSA-gold, 100% humidity, -1.5 to -5 micron defocus"},{"descriptionType":"Other","description":"08_dose-filt.st,  Tilt Series (Pixel Size 0.1778 nm), 2.3 GB\n\n08_dose-filt.rec,  Reconstruction (Pixel Size 0.7112 nm), 129.2 MB\n\nTS_08.mrc.mdoc,  24.8 kB\n\nframes.tar.bz2,  zipped raw frames, 2.3 GB\n\nscripts.tar.bz2,  zipped processing scripts, 5.3 kB"}],"geoLocations":[],"fundingReferences":[{"funderName":"NIH"},{"funderName":"HHMI"},{"funderName":"Beckman Institute"},{"funderIdentifierType":"ROR","funderName":"Gordon and Betty Moore Foundation","funderIdentifier":"006wxqw41"},{"funderIdentifierType":"ROR","funderName":"Agouron Institute","funderIdentifier":"05vmwhp17"},{"funderIdentifierType":"ROR","funderName":"John Templeton Foundation","funderIdentifier":"035tnyy05"}],"url":"https://data.caltech.edu/doi/10.22002/gyq44-bq059","contentUrl":null,"metadataVersion":2,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"api","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2023-06-09T16:27:24Z","registered":"2023-06-09T16:27:25Z","published":null,"updated":"2026-06-26T22:57:01Z"},"relationships":{"client":{"data":{"id":"caltech.data","type":"clients"}}}},{"id":"10.22002/64dmw-fhs97","type":"dois","attributes":{"doi":"10.22002/64dmw-fhs97","identifiers":[{"identifier":"oai:data.caltech.edu:64dmw-fhs97","identifierType":"oai"},{"identifier":"swj2018-07-31-5","identifierType":"tiltid"}],"creators":[{"nameType":"Personal","affiliation":["California Institute of Technology"],"givenName":"Sara","familyName":"Weaver","name":"Weaver, Sara","nameIdentifiers":[]}],"titles":[{"title":"Vibrio cholerae SAD2112"}],"publisher":"CaltechDATA","container":{},"publicationYear":2018,"subjects":[{"subject":"Vibrio cholerae"},{"subject":"SAD2112"},{"subject":"Single Axis"},{"subject":"Caltech Polara"},{"subject":"SerialEM"},{"subject":"pipeline"},{"subject":"Raptor"}],"contributors":[],"dates":[{"date":"2018","dateType":"Issued"},{"date":"2018-07-31","dateType":"Collected"},{"date":"2018-07-31","dateType":"Created"},{"date":"2018-08-01","dateType":"Updated"}],"language":"en","types":{"schemaOrg":"Dataset","resourceTypeGeneral":"Dataset","citeproc":"dataset","bibtex":"misc","ris":"DATA","resourceType":""},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":["jpg","mp4","rec","mrc"],"version":null,"rightsList":[{"rightsIdentifierScheme":"SPDX","rightsUri":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rights":"Creative Commons Attribution Non Commercial 4.0 International","rightsIdentifier":"cc-by-nc-4.0"}],"descriptions":[{"descriptionType":"Abstract","description":"SAD2112 (for T2SS only) = rpoS*, lacZ::lacIq, comEA-mCherry, ΔluxO, Ptac-tfoX, Ptac-recA, ∆TCP::ZeoR, ∆MSHA::CarbR, ∆CTX::KanR, ∆pilMNOPQ::TmR (aka ∆competence pilus) Ankur: \"For the taxonomy ID - unfortunately the strain we sent does not have a taxonomy ID. So, you can use the generic one for V. cholerae which is \"666\". The strain we are working with is related to N16961, but is certainly not the same strain, so not sure if you would want to indicate that somehow? Just for reference - the strain we sent is E7946 (although it is obviously heavily modified with a number of mutations). \""},{"descriptionType":"TechnicalInfo","description":"Tilt Series Date: 2018-07-31\nData Taken By: Sara Weaver\nSpecies / Specimen: Vibrio cholerae\nStrain: SAD2112\nTilt Series Settings:  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 180.0 eV/Ų,  defocus: -6.0 μm,  magnification: 27500x. \nMicroscope: Caltech Polara\nAcquisition Software: SerialEM\nUpload Method: pipeline\nProcessing Software Used: Raptor\nCollaborators and Roles: Strain from Ankur B Dalia ankdalia@indiana.edu, PhD, Assistant Professor, Indiana University. Cells grown, data collected by Sara Weaver\nPurification / Growth Conditions / Treatment: Streaked stock on a plate. Grew up a single colony in 3 mL LB with shaking at 37˚C. The next day, subcultured 50uL of this overnight culture into 3mL of fresh LB+100uM IPTG + 20mM MgCl2 + 10mM CaCl2 and grow at 30˚C shaking for ~4 hours.  Note that the induction wasn't necessary for this delta T4 competence pili strain\nSample Preparation: On 2018/07/12 spun gold (100 µL 10 nm gold + 25 µL 5% BSA) at 15,000rpm for 20 minutes, removed supernatant. Resuspended gold beads in 20 µL liquid culture. Vitrobot RT and 95% humidity, 3µL of gold/sample slurry on carbon/copper Quantifoil Finder grids R2/2 (EmiTech glow discharge 50 mA 120 s) Blot force +6, blot time 3 s, no waiting time, no drain time. Plunged into ethane/propane mix."},{"descriptionType":"Other","description":"2112I_tomogram5.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.1 GB\n\n2112I_tomogram5_part38_4.rec,  Reconstruction (Pixel Size 1.56 nm), 444.5 MB"}],"geoLocations":[],"fundingReferences":[{"funderName":"NIH"},{"funderName":"HHMI"},{"funderName":"Beckman Institute"},{"funderIdentifierType":"ROR","funderName":"Gordon and Betty Moore Foundation","funderIdentifier":"006wxqw41"},{"funderIdentifierType":"ROR","funderName":"Agouron Institute","funderIdentifier":"05vmwhp17"},{"funderIdentifierType":"ROR","funderName":"John Templeton Foundation","funderIdentifier":"035tnyy05"}],"url":"https://data.caltech.edu/doi/10.22002/64dmw-fhs97","contentUrl":null,"metadataVersion":2,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"api","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2023-06-09T16:27:59Z","registered":"2023-06-09T16:28:00Z","published":null,"updated":"2026-06-26T22:56:55Z"},"relationships":{"client":{"data":{"id":"caltech.data","type":"clients"}}}},{"id":"10.22002/cw45h-4da43","type":"dois","attributes":{"doi":"10.22002/cw45h-4da43","identifiers":[{"identifier":"oai:data.caltech.edu:cw45h-4da43","identifierType":"oai"},{"identifier":"dga2019-12-05-41","identifierType":"tiltid"}],"creators":[{"nameType":"Personal","affiliation":["California Institute of Technology"],"givenName":"Debnath","familyName":"Ghosal","name":"Ghosal, Debnath","nameIdentifiers":[]}],"titles":[{"title":"JV9082_K3_janelia"}],"publisher":"CaltechDATA","container":{},"publicationYear":2019,"subjects":[{"subject":"Legionella pneumophila"},{"subject":"Philadelphia-1_Lp02"},{"subject":"Single Axis"},{"subject":"Janelia Titan"},{"subject":"SerialEM"},{"subject":"pipeline"},{"subject":"Raptor"}],"contributors":[],"dates":[{"date":"2019","dateType":"Issued"},{"date":"2019-12-05","dateType":"Collected"},{"date":"2020-07-05","dateType":"Created"},{"date":"2020-07-07","dateType":"Updated"}],"language":"en","types":{"schemaOrg":"Dataset","resourceTypeGeneral":"Dataset","citeproc":"dataset","bibtex":"misc","ris":"DATA","resourceType":""},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":["rec","mrc","mp4","jpg"],"version":null,"rightsList":[{"rightsIdentifierScheme":"SPDX","rightsUri":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rights":"Creative Commons Attribution Non Commercial 4.0 International","rightsIdentifier":"cc-by-nc-4.0"}],"descriptions":[{"descriptionType":"Abstract","description":"JV9082:DotF-sfGFP fusion"},{"descriptionType":"TechnicalInfo","description":"Tilt Series Date: 2019-12-05\nData Taken By: Debnath Ghosal\nSpecies / Specimen: Legionella pneumophila\nStrain: Philadelphia-1_Lp02\nTilt Series Settings:  Single Axis, tilt range: (-54.0°, 54.0°), step: 3.0°, constant angular increment, dosage: 90.0 eV/Ų,  defocus: -4.0 μm,  magnification: 26000x. \nMicroscope: Janelia Titan\nAcquisition Software: SerialEM\nUpload Method: pipeline\nProcessing Software Used: Raptor\nCollaborators and Roles: Strain sent to us by Joseph P. 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The original data (images) consists of 10 different corn growing PhenoCam sites in US, which were annotated for growth stage labeling manually based on visual appearance. \nThe intermediate model output includes learning curves (training and validation log), and predictions of test images, for respective deep learning (DL) models (4) across individual PhenoCam sites (10) and image clipping levels (5). The final results after model development and testing comprise confusion matrices and classification reports. \n\nThe lightweight DL models developed for this study are ELiteCrop0, ELiteCrop1, ELiteCrop4, and MobNetCropV2 using transfer learning techniques. The results are based on site-wise and five PhenoCam image clipping levels (0-40%) across individual models. The dataset provides model performance evaluation results based on intrasite (training and testing on the same PhenoCam site) and intersite (testing on a new PhenoCam site) methods. Initially, models were developed using a supercomputer (CCAST, NDSU), and they were finally deployed on Raspberry Pi (single board computer). The dataset documents the implementation and performance of the finalized model (ELiteCrop0) deployed on Raspberry Pi, including inference time, computational efficiency, and hardware utilization metrics.\n\nThe contents of the dataset include: 1. Abstract, 2. PhenoCam data annotation visual class labels, 3. Training and validation accuracy and loss curves, 4. Confusion matrix plots, 5. Sample prediction plots, 6. Classification report, 7. CPU timing, 8. Sample prediction plots for Raspberry Pi, 9. Intersite evaluation with ELiteCrop0, and 10. 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These are wild type cells but they . don't express complete FliP protein. Therefore, they don't assemble full flagella. We knocked out FliM protein . of the flagellar motor to study the early assembly states of flagellar motor.\nPurification / Growth Conditions / Treatment: I grew the cells on blood agar plates from -80 stock at 37C with 5% CO2. the cells were grown . for 48 hours and then spread on a new plate with a cotton swab and left to grow for 24 hours. . The grids were prepared from both batches (48 hours, and 24 hours, separately).\nSample Preparation: The samples were prepared with Vitrobot IV. Blotting conditions were either: blot force 6, blot . time 3, drain time 1 OR blot force -3, blot time 4, drain time 1, 100% humidity. Cu grids. 10 nm . gold."},{"descriptionType":"Other","description":"Hpylori_FliM_013_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 3.9 GB\n\nHpylori_FliM_013_af_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB"}],"geoLocations":[],"fundingReferences":[{"funderName":"NIH"},{"funderName":"HHMI"},{"funderName":"Beckman Institute"},{"funderIdentifierType":"ROR","funderName":"Gordon and Betty Moore Foundation","funderIdentifier":"006wxqw41"},{"funderIdentifierType":"ROR","funderName":"Agouron Institute","funderIdentifier":"05vmwhp17"},{"funderIdentifierType":"ROR","funderName":"John Templeton Foundation","funderIdentifier":"035tnyy05"}],"url":"https://data.caltech.edu/doi/10.22002/q8ssk-htw16","contentUrl":null,"metadataVersion":2,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"api","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2023-06-09T16:33:30Z","registered":"2023-06-09T16:33:31Z","published":null,"updated":"2026-06-26T22:55:59Z"},"relationships":{"client":{"data":{"id":"caltech.data","type":"clients"}}}},{"id":"10.22002/h98gr-rfh04","type":"dois","attributes":{"doi":"10.22002/h98gr-rfh04","identifiers":[{"identifier":"oai:data.caltech.edu:h98gr-rfh04","identifierType":"oai"},{"identifier":"mka2020-10-08-381","identifierType":"tiltid"}],"creators":[{"nameType":"Personal","affiliation":["California Institute of Technology"],"givenName":"Mohammed","familyName":"Kaplan","name":"Kaplan, Mohammed","nameIdentifiers":[]}],"titles":[{"title":"Hpylori_dFliF_FISE"}],"publisher":"CaltechDATA","container":{},"publicationYear":2020,"subjects":[{"subject":"Helicobacter pylori"},{"subject":"26695"},{"subject":"Single Axis"},{"subject":"Caltech Titan Krios"},{"subject":"Serial EM"},{"subject":"pipeline"},{"subject":"Raptor"}],"contributors":[],"dates":[{"date":"2020","dateType":"Issued"},{"date":"2020-10-08","dateType":"Collected"},{"date":"2020-10-13","dateType":"Created"},{"date":"2022-09-28","dateType":"Updated"}],"language":"en","types":{"schemaOrg":"Dataset","resourceTypeGeneral":"Dataset","citeproc":"dataset","bibtex":"misc","ris":"DATA","resourceType":""},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":["rec","jpg","mp4","mrc"],"version":null,"rightsList":[{"rightsIdentifierScheme":"SPDX","rightsUri":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rights":"Creative Commons Attribution Non Commercial 4.0 International","rightsIdentifier":"cc-by-nc-4.0"}],"descriptions":[{"descriptionType":"Abstract","description":"These are H_pylori cells that are lacking FliP protein. In these cells, FliF protein was knocked out  .  to examine its relation to the hat-like complex."},{"descriptionType":"TechnicalInfo","description":"Tilt Series Date: 2020-10-08\nData Taken By: Mohammed Kaplan\nSpecies / Specimen: Helicobacter pylori\nStrain: 26695\nTilt Series Settings:  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 120.0 eV/Ų,  defocus: -8.0 μm,  magnification: 19500x. \nMicroscope: Caltech Titan Krios\nAcquisition Software: Serial EM\nUpload Method: pipeline\nProcessing Software Used: Raptor\nCollaborators and Roles: The cells were prepared and sent by Carrie Schaffer from the university of Kentucky. The cells were grown at 37C with 5% CO2 on sheep blood agar plates for 2 days from a -80C. No growth was seen . on the plates after 24 hr therefore the plates were kept in the . incubator for another 24Hr.\nPurification / Growth Conditions / Treatment: The samples were prepared with Vitrobot IV. Blotting conditions were either: blot force 6, blot . time 3, drain time 1 OR blot force -3, blot time 4, drain time 1, 100%  humidity. Cu grids. 10 nm . gold"},{"descriptionType":"Other","description":"Hpylori_DFliF_FISE_386.mrc,  Tilt Series (Pixel Size 0.452 nm), 1.9 GB\n\nHpylori_DFliF_FISE_386_full.rec,  Reconstruction (Pixel Size 1.808 nm), 737.3 MB"}],"geoLocations":[],"fundingReferences":[{"funderName":"NIH"},{"funderName":"HHMI"},{"funderName":"Beckman Institute"},{"funderIdentifierType":"ROR","funderName":"Gordon and Betty Moore Foundation","funderIdentifier":"006wxqw41"},{"funderIdentifierType":"ROR","funderName":"Agouron Institute","funderIdentifier":"05vmwhp17"},{"funderIdentifierType":"ROR","funderName":"John Templeton Foundation","funderIdentifier":"035tnyy05"}],"url":"https://data.caltech.edu/doi/10.22002/h98gr-rfh04","contentUrl":null,"metadataVersion":2,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"api","isActive":true,"state":"findable","reason":null,"viewCount":0,"downloadCount":0,"referenceCount":0,"citationCount":0,"partCount":0,"partOfCount":0,"versionCount":0,"versionOfCount":0,"created":"2023-06-09T16:33:59Z","registered":"2023-06-09T16:33:59Z","published":null,"updated":"2026-06-26T22:55:53Z"},"relationships":{"client":{"data":{"id":"caltech.data","type":"clients"}}}},{"id":"10.22002/6t8ng-1vz65","type":"dois","attributes":{"doi":"10.22002/6t8ng-1vz65","identifiers":[{"identifier":"oai:data.caltech.edu:6t8ng-1vz65","identifierType":"oai"},{"identifier":"wnj2020-09-29-21","identifierType":"tiltid"}],"creators":[{"nameType":"Personal","affiliation":["California Institute of Technology"],"givenName":"William","familyName":"Nicolas","name":"Nicolas, William","nameIdentifiers":[]}],"titles":[{"title":"lip10-2 (+ megacomplex)"}],"publisher":"CaltechDATA","container":{},"publicationYear":2020,"subjects":[{"subject":"Escherichia coli"},{"subject":"PK2, BL21 dHisdHA RQABpCDF+EFGpRSF"},{"subject":"Single Axis"},{"subject":"IECB Talos Artica"},{"subject":"Serial EM"},{"subject":"pipeline"},{"subject":"Raptor"}],"contributors":[],"dates":[{"date":"2020","dateType":"Issued"},{"date":"2020-09-29","dateType":"Collected"},{"date":"2020-11-16","dateType":"Created"},{"date":"2020-11-20","dateType":"Updated"}],"language":"en","types":{"schemaOrg":"Dataset","resourceTypeGeneral":"Dataset","citeproc":"dataset","bibtex":"misc","ris":"DATA","resourceType":""},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":["rec","mrc","mp4","jpg"],"version":null,"rightsList":[{"rightsIdentifierScheme":"SPDX","rightsUri":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rights":"Creative Commons Attribution Non Commercial 4.0 International","rightsIdentifier":"cc-by-nc-4.0"}],"descriptions":[{"descriptionType":"Abstract","description":"Exposure 1-1.3s"},{"descriptionType":"TechnicalInfo","description":"Tilt Series Date: 2020-09-29\nData Taken By: William Nicolas\nSpecies / Specimen: Escherichia coli\nStrain: PK2, BL21 dHisdHA RQABpCDF+EFGpRSF\nTilt Series Settings:  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 56.0 eV/Ų,  defocus: -8.0 μm,  magnification: 11000x. \nMicroscope: IECB Talos Artica\nAcquisition Software: Serial EM\nUpload Method: pipeline\nProcessing Software Used: Raptor\nCollaborators and Roles: Petya Krasteva (head of the SBB lab at the IECB, Bordeaux° and Wiem . Abidi (graduate student) did the preps and helped with acquisition\nPurification / Growth Conditions / Treatment: BL21 cells were transformed with QAB - pCDF plasmid and EFG - pRSF . plasmid to express the inner-membrane macro-complex.. . Selection done with Kanamycin and Streptomycin.. . Induction of expression ON done with IPTG. . Spheroplasts are generated from the BL21 non transformed cells cells.. Spheroplasts are processed through a high-pressure homogenizer and . further purification by ultracentrifugation of the membrane . fractions. . Liposomes are then generated from the membrane fractions by . processing through Potter and sonicator.. \nSample Preparation: Fiducials were prepared my method (see lab archive). . Grids: Quantifoil Cu NH2 R2/2. . Glowdischarged 3mA - 2min. BT3s - BF0. 4uL pipetted on the grids"},{"descriptionType":"Other","description":"lip10-2-sq2-tg3.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.7 GB\n\nlip10-2-sq2-tg3_full.rec,  Reconstruction (Pixel Size 0.78 nm), 1.8 GB"}],"geoLocations":[],"fundingReferences":[{"funderName":"NIH"},{"funderName":"HHMI"},{"funderName":"Beckman Institute"},{"funderIdentifierType":"ROR","funderName":"Gordon and Betty Moore Foundation","funderIdentifier":"006wxqw41"},{"funderIdentifierType":"ROR","funderName":"Agouron Institute","funderIdentifier":"05vmwhp17"},{"funderIdentifierType":"ROR","funderName":"John Templeton 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Georges","nameIdentifiers":[]}],"titles":[{"title":"P. gingivalis wild type"}],"publisher":"CaltechDATA","container":{},"publicationYear":2020,"subjects":[{"subject":"Porphyromonas gingivalis"},{"subject":"Single Axis"},{"subject":"Caltech Titan Krios"},{"subject":"Serial EM"},{"subject":"pipeline"},{"subject":"Raptor"}],"contributors":[],"dates":[{"date":"2020","dateType":"Issued"},{"date":"2020-11-06","dateType":"Collected"},{"date":"2020-11-07","dateType":"Created"},{"date":"2022-09-05","dateType":"Updated"}],"language":"en","types":{"schemaOrg":"Dataset","resourceTypeGeneral":"Dataset","citeproc":"dataset","bibtex":"misc","ris":"DATA","resourceType":""},"relatedIdentifiers":[],"relatedItems":[],"sizes":[],"formats":["jpg","rec","mp4","mrc"],"version":null,"rightsList":[{"rightsIdentifierScheme":"SPDX","rightsUri":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rights":"Creative Commons Attribution Non Commercial 4.0 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In these cells, FliF protein was knocked out  .  to examine its relation to the hat-like complex."},{"descriptionType":"TechnicalInfo","description":"Tilt Series Date: 2020-10-08\nData Taken By: Mohammed Kaplan\nSpecies / Specimen: Helicobacter pylori\nStrain: 26695\nTilt Series Settings:  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 120.0 eV/Ų,  defocus: -8.0 μm,  magnification: 19500x. \nMicroscope: Caltech Titan Krios\nAcquisition Software: Serial EM\nUpload Method: pipeline\nProcessing Software Used: None\nCollaborators and Roles: The cells were prepared and sent by Carrie Schaffer from the university of Kentucky.\nPurification / Growth Conditions / Treatment: The cells were grown at 37C with 5% CO2 on sheep blood agar plates for 2 days from a -80C . stock. No growth was seen on the plates after 24 hr therefore the plates were kept in the . incubator for another 24Hr.\nSample Preparation: The samples were prepared with Vitrobot IV. Blotting conditions were either: blot force 6, blot . time 3, drain time 1 OR blot force -3, blot time 4, drain time 1, 100%  humidity. 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