cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.3991922
title: Slidescans: p176

description: This repository constains all the slidescans associated with slide block p176 for the project: <strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong> Vito RT Zanotelli<br> Matthias Leutenegger<br> Xiao‐Kang Lun<br> Fanny Georgi<br> Natalie de Souza<br> Bernd Bodenmiller <em>Mol Syst Biol. (2020) 16: e9798</em><br> https://doi.org/10.15252/msb.20209798 <em>Please cite this article if you re-use any of the data or code.</em> Each acquisition follows the naming scheme: "{operator}_{date}_{slideblock}_{slidescan_flo_number}{suffix}" e.g. v.zanotelli_20190509_p161_025.czi With: operator: the slidescan operator date: the acquisition date slideblock: the block cut to produce these slides slidescan_fluo_nr: arbitrary index. Is matched to actual slide number using the metadata file: '20190506_bigstain_selection_final_if_imcalign_v1.csv' suffix: '.czi': main slidescan '_pt1.czi': scan of handwritten slide label '_pt2.csi': coarse slide overview scan Each 'main slidescan' is usually composed of multiple 'scenes' (regions that were scanned with high resolution). The convention is that each scene corresponds to unique cut that is independently stained. Note that scene numbering is not sequential but rather random. The slidescans were acquired using an AxioScan.Z1 microscope with: Objective: Plan-Apochromat 20x/0.8 M27 Resolution: nominal 0.325 um/pixel Channels: 1) DAPI: Excitation Wavelength: 353 nm, Emission Wavelength: 465 nm
DOI: 10.5281/zenodo.4066430
title: Slidescans: p161

description: This repository constains all the slidescans associated with slide block p161 for the project: <strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong> Vito RT Zanotelli<br> Matthias Leutenegger<br> Xiao‐Kang Lun<br> Fanny Georgi<br> Natalie de Souza<br> Bernd Bodenmiller <em>Mol Syst Biol. (2020) 16: e9798</em><br> https://doi.org/10.15252/msb.20209798 <em>Please cite this article if you re-use any of the data or code.</em> Each acquisition follows the naming scheme: "{operator}_{date}_{slideblock}_{slidenr}{suffix}" e.g. v.zanotelli_20190509_p161_025.czi Each acquisition has 3 files: - suffix='.czi': main slidescan - suffix='_pt1.czi': slide label scan - suffix='_pt2.csi': coarse slide overview scan Each 'main slidescan' is usually composed of multiple 'Scenes', corresponding to regions scanned with high resolution. The convention is that each scene corresponds to unique cut that is independently stained and processed. Note that scene numbering does not necessarily follows a logical order. The slidescans were acquired using an AxioScan A1 <br>
DOI: 10.5281/zenodo.3991916
title: Slidescans: p161

description: This repository constains all the slidescans associated with slide block p161 for the project: <strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong> Vito RT Zanotelli<br> Matthias Leutenegger<br> Xiao‐Kang Lun<br> Fanny Georgi<br> Natalie de Souza<br> Bernd Bodenmiller <em>Mol Syst Biol. (2020) 16: e9798</em><br> https://doi.org/10.15252/msb.20209798 <em>Please cite this article if you re-use any of the data or code.</em> Each acquisition follows the naming scheme: "{operator}_{date}_{slideblock}_{slidenr}{suffix}" e.g. v.zanotelli_20190509_p161_025.czi Each acquisition has 3 files: - suffix='.czi': main slidescan - suffix='_pt1.czi': slide label scan - suffix='_pt2.csi': coarse slide overview scan Each 'main slidescan' is usually composed of multiple 'Scenes', corresponding to regions scanned with high resolution. The convention is that each scene corresponds to unique cut that is independently stained and processed. Note that scene numbering does not necessarily follows a logical order. The slidescans were acquired using an AxioScan A1 <br>
DOI: 10.5281/zenodo.3991919
title: Slidescans: p165

description: This repository constains all the slidescans associated with slide block p165 for the project: <strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong> Vito RT Zanotelli<br> Matthias Leutenegger<br> Xiao‐Kang Lun<br> Fanny Georgi<br> Natalie de Souza<br> Bernd Bodenmiller <em>Mol Syst Biol. (2020) 16: e9798</em><br> https://doi.org/10.15252/msb.20209798 <em>Please cite this article if you re-use any of the data or code.</em> Each acquisition follows the naming scheme: "{operator}_{date}_{slideblock}_{slidescan_flo_number}{suffix}" e.g. v.zanotelli_20190509_p161_025.czi With: operator: the slidescan operator date: the acquisition date slideblock: the block cut to produce these slides slidescan_fluo_nr: arbitrary index. Is matched to actual slide number using the metadata file: '20190506_bigstain_selection_final_if_imcalign_v1.csv' suffix: '.czi': main slidescan '_pt1.czi': scan of handwritten slide label '_pt2.csi': coarse slide overview scan Each 'main slidescan' is usually composed of multiple 'scenes' (regions that were scanned with high resolution). The convention is that each scene corresponds to unique cut that is independently stained. Note that scene numbering is not sequential but rather random. The slidescans were acquired using an AxioScan.Z1 microscope with: Objective: Plan-Apochromat 20x/0.8 M27 Resolution: nominal 0.325 um/pixel Channels: 1) EGFP: Excitation Wavelength: 488 nm, Emission Wavelength: 509 nm 2) DAPI: Excitation Wavelength: 353 nm, Emission Wavelength: 465 nm
DOI: 10.5281/zenodo.3991918
title: Slidescans: p165

description: This repository constains all the slidescans associated with slide block p165 for the project: <strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong> Vito RT Zanotelli<br> Matthias Leutenegger<br> Xiao‐Kang Lun<br> Fanny Georgi<br> Natalie de Souza<br> Bernd Bodenmiller <em>Mol Syst Biol. (2020) 16: e9798</em><br> https://doi.org/10.15252/msb.20209798 <em>Please cite this article if you re-use any of the data or code.</em> Each acquisition follows the naming scheme: "{operator}_{date}_{slideblock}_{slidescan_flo_number}{suffix}" e.g. v.zanotelli_20190509_p161_025.czi With: operator: the slidescan operator date: the acquisition date slideblock: the block cut to produce these slides slidescan_fluo_nr: arbitrary index. Is matched to actual slide number using the metadata file: '20190506_bigstain_selection_final_if_imcalign_v1.csv' suffix: '.czi': main slidescan '_pt1.czi': scan of handwritten slide label '_pt2.csi': coarse slide overview scan Each 'main slidescan' is usually composed of multiple 'scenes' (regions that were scanned with high resolution). The convention is that each scene corresponds to unique cut that is independently stained. Note that scene numbering is not sequential but rather random. The slidescans were acquired using an AxioScan.Z1 microscope with: Objective: Plan-Apochromat 20x/0.8 M27 Resolution: nominal 0.325 um/pixel Channels: 1) EGFP: Excitation Wavelength: 488 nm, Emission Wavelength: 509 nm 2) DAPI: Excitation Wavelength: 353 nm, Emission Wavelength: 465 nm
DOI: 10.5281/zenodo.4396288
title: Endurance and Avoidance Response Patterns in Pain Patients: Application of Action Control Theory in Pain Research

description: Identifying pain-related response patterns and understanding underlying functional mechanisms of symptom formation and recovery are essential steps for tailoring interventions to increase the effectiveness of treatment. The focus of this study thus was to replicate pain-related avoidance and endurance response patterns associated with the Fear-Avoidance Model (FAM) and Avoidance-Endurance Model (AEM) by means of latent profile analysis. Apart from the analysis of primary and other secondary characteristics of the pain response profiles, we especially analyzed the influence of stress and action control as covariates in accordance with Action Control Theory (ACT).
description: The data acquisition for this project was funded by the German Pension Insurance (Deutsche Rentenversicherung Bund) and the Federal Ministry of Education and Research (BMBF) within the research priority "Chronic diseases and patient orientation" - Grant number: 0421-FSCP-0529.
DOI: 10.5281/zenodo.4396287
title: Endurance and Avoidance Response Patterns in Pain Patients: Application of Action Control Theory in Pain Research

description: Identifying pain-related response patterns and understanding underlying functional mechanisms of symptom formation and recovery are essential steps for tailoring interventions to increase the effectiveness of treatment. The focus of this study thus was to replicate pain-related avoidance and endurance response patterns associated with the Fear-Avoidance Model (FAM) and Avoidance-Endurance Model (AEM) by means of latent profile analysis. Apart from the analysis of primary and other secondary characteristics of the pain response profiles, we especially analyzed the influence of stress and action control as covariates in accordance with Action Control Theory (ACT).
description: The data acquisition for this project was funded by the German Pension Insurance (Deutsche Rentenversicherung Bund) and the Federal Ministry of Education and Research (BMBF) within the research priority "Chronic diseases and patient orientation" - Grant number: 0421-FSCP-0529.
DOI: 10.5281/zenodo.3991945
title: Spillover: physiology: p173, p176

description: This contains two acquisitions of single spotted metals acquired concurently with the IMC acquisitions for p173, p176 for the publication: <strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong> Vito RT Zanotelli<br> Matthias Leutenegger<br> Xiao‐Kang Lun<br> Fanny Georgi<br> Natalie de Souza<br> Bernd Bodenmiller <em>Mol Syst Biol. (2020) 16: e9798</em><br> https://doi.org/10.15252/msb.20209798 <em>Please cite this article if you re-use any of the data or code.</em> The metals were spotted according to: https://docs.google.com/document/d/11VP3n3ulaSCSXemreJWh66-ogcB5BveHH5gTXAykXgQ/edit?usp=sharing, as described in the paper: "Compensation of signal spillover in suspension and imaging mass cytometry" by Stéphane Chevrier*, Helena L. Crowell*, Vito R.T. Zanotelli*, Stefanie Engler, Mark D. Robinson, and Bernd Bodenmiller which is published in 'Cell Systems' as "Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry" (http://www.cell.com/cell-systems/abstract/S2405-4712(18)30063-2)
DOI: 10.5281/zenodo.3991944
title: Spillover: physiology: p173, p176

description: This contains two acquisitions of single spotted metals acquired concurently with the IMC acquisitions for p173, p176 for the publication: <strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong> Vito RT Zanotelli<br> Matthias Leutenegger<br> Xiao‐Kang Lun<br> Fanny Georgi<br> Natalie de Souza<br> Bernd Bodenmiller <em>Mol Syst Biol. (2020) 16: e9798</em><br> https://doi.org/10.15252/msb.20209798 <em>Please cite this article if you re-use any of the data or code.</em> The metals were spotted according to: https://docs.google.com/document/d/11VP3n3ulaSCSXemreJWh66-ogcB5BveHH5gTXAykXgQ/edit?usp=sharing, as described in the paper: "Compensation of signal spillover in suspension and imaging mass cytometry" by Stéphane Chevrier*, Helena L. Crowell*, Vito R.T. Zanotelli*, Stefanie Engler, Mark D. Robinson, and Bernd Bodenmiller which is published in 'Cell Systems' as "Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry" (http://www.cell.com/cell-systems/abstract/S2405-4712(18)30063-2)
DOI: 10.5281/zenodo.3991947
title: Spillover acquisitions: oexp: p161, p165

description: This contains two acquisitions of single spotted metals acquired concurently with the IMC acquisitions for p173, p176 for the publication: <strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong> Vito RT Zanotelli<br> Matthias Leutenegger<br> Xiao‐Kang Lun<br> Fanny Georgi<br> Natalie de Souza<br> Bernd Bodenmiller <em>Mol Syst Biol. (2020) 16: e9798</em><br> https://doi.org/10.15252/msb.20209798 <em>Please cite this article if you re-use any of the data or code.</em> The metals were spotted according to: https://docs.google.com/document/d/11VP3n3ulaSCSXemreJWh66-ogcB5BveHH5gTXAykXgQ/edit?usp=sharing, as described in the paper: "Compensation of signal spillover in suspension and imaging mass cytometry" by Stéphane Chevrier*, Helena L. Crowell*, Vito R.T. Zanotelli*, Stefanie Engler, Mark D. Robinson, and Bernd Bodenmiller which is published in 'Cell Systems' as "Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry" (http://www.cell.com/cell-systems/abstract/S2405-4712(18)30063-2)
DOI: 10.5281/zenodo.3991946
title: Spillover acquisitions: oexp: p161, p165

description: This contains two acquisitions of single spotted metals acquired concurently with the IMC acquisitions for p173, p176 for the publication: <strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong> Vito RT Zanotelli<br> Matthias Leutenegger<br> Xiao‐Kang Lun<br> Fanny Georgi<br> Natalie de Souza<br> Bernd Bodenmiller <em>Mol Syst Biol. (2020) 16: e9798</em><br> https://doi.org/10.15252/msb.20209798 <em>Please cite this article if you re-use any of the data or code.</em> The metals were spotted according to: https://docs.google.com/document/d/11VP3n3ulaSCSXemreJWh66-ogcB5BveHH5gTXAykXgQ/edit?usp=sharing, as described in the paper: "Compensation of signal spillover in suspension and imaging mass cytometry" by Stéphane Chevrier*, Helena L. Crowell*, Vito R.T. Zanotelli*, Stefanie Engler, Mark D. Robinson, and Bernd Bodenmiller which is published in 'Cell Systems' as "Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry" (http://www.cell.com/cell-systems/abstract/S2405-4712(18)30063-2)
DOI: 10.5281/zenodo.3991937
title: Imaging Mass Cytometry: p173

description: Imaging Mass Cytometry: p173 Raw acquisitions for the paper: <strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong> Vito RT Zanotelli<br> Matthias Leutenegger<br> Xiao‐Kang Lun<br> Fanny Georgi<br> Natalie de Souza<br> Bernd Bodenmiller <em>Mol Syst Biol. (2020) 16: e9798</em><br> https://doi.org/10.15252/msb.20209798 <em>Please cite this article if you re-use any of the data or code.</em>
DOI: 10.5281/zenodo.3991936
title: Imaging Mass Cytometry: p173

description: Imaging Mass Cytometry: p173 Raw acquisitions for the paper: <strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong> Vito RT Zanotelli<br> Matthias Leutenegger<br> Xiao‐Kang Lun<br> Fanny Georgi<br> Natalie de Souza<br> Bernd Bodenmiller <em>Mol Syst Biol. (2020) 16: e9798</em><br> https://doi.org/10.15252/msb.20209798 <em>Please cite this article if you re-use any of the data or code.</em>
DOI: 10.5281/zenodo.3991939
title: Imaging Mass Cytometry: p176

description: Imaging Mass Cytometry: p176 Raw acquisitions for the paper: <strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong> Vito RT Zanotelli<br> Matthias Leutenegger<br> Xiao‐Kang Lun<br> Fanny Georgi<br> Natalie de Souza<br> Bernd Bodenmiller <em>Mol Syst Biol. (2020) 16: e9798</em><br> https://doi.org/10.15252/msb.20209798 <em>Please cite this article if you re-use any of the data or code.</em>
DOI: 10.5281/zenodo.3991938
title: Imaging Mass Cytometry: p176

description: Imaging Mass Cytometry: p176 Raw acquisitions for the paper: <strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong> Vito RT Zanotelli<br> Matthias Leutenegger<br> Xiao‐Kang Lun<br> Fanny Georgi<br> Natalie de Souza<br> Bernd Bodenmiller <em>Mol Syst Biol. (2020) 16: e9798</em><br> https://doi.org/10.15252/msb.20209798 <em>Please cite this article if you re-use any of the data or code.</em>
DOI: 10.5281/zenodo.3991933
title: Imaging Mass Cytometry: p161

description: Imaging Mass Cytometry: p161 Raw acquisitions for the paper: <strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong> Vito RT Zanotelli<br> Matthias Leutenegger<br> Xiao‐Kang Lun<br> Fanny Georgi<br> Natalie de Souza<br> Bernd Bodenmiller <em>Mol Syst Biol. (2020) 16: e9798</em><br> https://doi.org/10.15252/msb.20209798 <em>Please cite this article if you re-use any of the data or code.</em>
DOI: 10.5281/zenodo.3991932
title: Imaging Mass Cytometry: p161

description: Imaging Mass Cytometry: p161 Raw acquisitions for the paper: <strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong> Vito RT Zanotelli<br> Matthias Leutenegger<br> Xiao‐Kang Lun<br> Fanny Georgi<br> Natalie de Souza<br> Bernd Bodenmiller <em>Mol Syst Biol. (2020) 16: e9798</em><br> https://doi.org/10.15252/msb.20209798 <em>Please cite this article if you re-use any of the data or code.</em>
DOI: 10.5281/zenodo.3991935
title: Imaging Mass Cytometry: p165

description: Imaging Mass Cytometry: p165 Raw acquisitions for the paper: <strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong> Vito RT Zanotelli<br> Matthias Leutenegger<br> Xiao‐Kang Lun<br> Fanny Georgi<br> Natalie de Souza<br> Bernd Bodenmiller <em>Mol Syst Biol. (2020) 16: e9798</em><br> https://doi.org/10.15252/msb.20209798 <em>Please cite this article if you re-use any of the data or code.</em>
DOI: 10.5281/zenodo.3991934
title: Imaging Mass Cytometry: p165

description: Imaging Mass Cytometry: p165 Raw acquisitions for the paper: <strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong> Vito RT Zanotelli<br> Matthias Leutenegger<br> Xiao‐Kang Lun<br> Fanny Georgi<br> Natalie de Souza<br> Bernd Bodenmiller <em>Mol Syst Biol. (2020) 16: e9798</em><br> https://doi.org/10.15252/msb.20209798 <em>Please cite this article if you re-use any of the data or code.</em>
DOI: 10.5281/zenodo.3991929
title: Brightfield images: p173

description: This repository constains all the brightfield plate scans plate p173 for the project: <strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong> Vito RT Zanotelli<br> Matthias Leutenegger<br> Xiao‐Kang Lun<br> Fanny Georgi<br> Natalie de Souza<br> Bernd Bodenmiller <em>Mol Syst Biol. (2020) 16: e9798</em><br> https://doi.org/10.15252/msb.20209798 <em>Please cite this article if you re-use any of the data or code.</em> Each plate acquisition follows the naming scheme: '{date}-{operator}-Spheroid-{plate}[rev]-{dps}-ac{acnr}_Plate_{acquisitionid} eg. 20180203-Vito-Spheroid-p173-2dps-ac1_Plate_13146 20180204-Vito-Spheroid-p173rev-3dps-ac1_Plate_1315 With: date: acquisition date operator: microscope operator plate: plate number rev: optional, if there indicates that the plate has been rotated 180 degree. E.g. well A01 will be well H12. dps: days post seeding ac: manual acquisition number (e.g. if acquisition needed to be repeated) acquisitionid: machine provided unique acquisition id Each folder contains: HTD files which contains acquisition metadata in text form. TimePoint_1: a folder containing all the acquisitions in .tiff form with the suffix _{wellname}_w{channel} In this acquisition 3 channels were used, which correspond to 3 brightfield images at 3 different z positions. An ImageXpress Micro XL Widefield High Content Imaging microscope (Molecular Devices, 4x objective, NA 0.20) was used for the acquisition.
DOI: 10.5281/zenodo.3991928
title: Brightfield images: p173

description: This repository constains all the brightfield plate scans plate p173 for the project: <strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong> Vito RT Zanotelli<br> Matthias Leutenegger<br> Xiao‐Kang Lun<br> Fanny Georgi<br> Natalie de Souza<br> Bernd Bodenmiller <em>Mol Syst Biol. (2020) 16: e9798</em><br> https://doi.org/10.15252/msb.20209798 <em>Please cite this article if you re-use any of the data or code.</em> Each plate acquisition follows the naming scheme: '{date}-{operator}-Spheroid-{plate}[rev]-{dps}-ac{acnr}_Plate_{acquisitionid} eg. 20180203-Vito-Spheroid-p173-2dps-ac1_Plate_13146 20180204-Vito-Spheroid-p173rev-3dps-ac1_Plate_1315 With: date: acquisition date operator: microscope operator plate: plate number rev: optional, if there indicates that the plate has been rotated 180 degree. E.g. well A01 will be well H12. dps: days post seeding ac: manual acquisition number (e.g. if acquisition needed to be repeated) acquisitionid: machine provided unique acquisition id Each folder contains: HTD files which contains acquisition metadata in text form. TimePoint_1: a folder containing all the acquisitions in .tiff form with the suffix _{wellname}_w{channel} In this acquisition 3 channels were used, which correspond to 3 brightfield images at 3 different z positions. An ImageXpress Micro XL Widefield High Content Imaging microscope (Molecular Devices, 4x objective, NA 0.20) was used for the acquisition.
DOI: 10.5281/zenodo.3991931
title: Brightfield images: p176

description: This repository constains all the brightfield plate scans plate p176 for the project: <strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong> Vito RT Zanotelli<br> Matthias Leutenegger<br> Xiao‐Kang Lun<br> Fanny Georgi<br> Natalie de Souza<br> Bernd Bodenmiller <em>Mol Syst Biol. (2020) 16: e9798</em><br> https://doi.org/10.15252/msb.20209798 <em>Please cite this article if you re-use any of the data or code.</em> Each plate acquisition follows the naming scheme: '{date}-{operator}-Spheroid-{plate}[rev]-{dps}-ac{acnr}_Plate_{acquisitionid} eg. 20180203-Vito-Spheroid-p173-2dps-ac1_Plate_13146 20180204-Vito-Spheroid-p173rev-3dps-ac1_Plate_1315 With: date: acquisition date operator: microscope operator plate: plate number rev: optional, if there indicates that the plate has been rotated 180 degree. E.g. well A01 will be well H12. dps: days post seeding ac: manual acquisition number (e.g. if acquisition needed to be repeated) acquisitionid: machine provided unique acquisition id Each folder contains: HTD files which contains acquisition metadata in text form. TimePoint_1: a folder containing all the acquisitions in .tiff form with the suffix _{wellname}_w{channel} In this acquisition 3 channels were used, which correspond to 3 brightfield images at 3 different z positions. An ImageXpress Micro XL Widefield High Content Imaging microscope (Molecular Devices, 4x objective, NA 0.20) was used for the acquisition.