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Dataset Nijmegen #18
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CMSOdataset2018-3DsphrdInvCollHT1080-Bakker/isa/Appendix I 3D spheroid culture.pdf
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CMSOdataset2018-3DsphrdInvCollHT1080-Bakker/isa/Appendix II Microscopy.pdf
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CMSOdataset2018-3DsphrdInvCollHT1080-Bakker/isa/Appendix III Image analysis (Extended).pdf
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...sa/a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N2.txt
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| Sample Name Protocol REF Parameter Value[imaging modality] Term Source REF Term Accession Number Parameter Value[imaging sequence type] Term Source REF Term Accession Number Parameter Value[observation period] Term Source REF Term Accession Number Unit Term Source REF Term Accession Number Parameter Value[channel definition] Parameter Value[objective lens] Parameter Value[numerical aperture] Raw Data File Parameter Value[PixelsizeX] Unit Term Source REF Term Accession Number Parameter Value[PixelsizeY] Unit Term Source REF Term Accession Number Parameter Value[PixelsizeZ] Unit Term Source REF Term Accession Number Protocol REF Data Transformation Name Derived Data File | ||
| B2_20x_medium_YAP_second image Appendix II Microscopy Scanning confocal microscopy PLOSTHES http://localhost/plosthes.2017-1#10559 single time point 24 h Ch1: YAP-AlexaFluor488, Ch2: Phalloidin-AlexaFluor633, Ch3: DAPI, Ch4: reflection, Ch5: transmission Zeiss Plan-Apochromat 20x/0.8NA 0.8 B2_20x_medium_YAP_second image_Raw.tar 1.2 �m 1.2 �m 2 �m https://github.com/Mverp/Cell3DMeasurements segmenttation, classification of migration phenotypes, calculation of cell specific and spheroid specific parameters B2_20x_medium_YAP_second image_Analysis.tar | ||
| B5_20x_medium_IgG_good settings Appendix II Microscopy Scanning confocal microscopy PLOSTHES http://localhost/plosthes.2017-1#10559 single time point 24 h Ch1: IgG1-AlexaFluor488, Ch2: Phalloidin-AlexaFluor633, Ch3: DAPI, Ch4: reflection, Ch5: transmission Zeiss Plan-Apochromat 20x/0.8NA 0.8 B5_20x_medium_IgG_good settings_Raw.tar 1.2 �m 1.2 �m 2 �m https://github.com/Mverp/Cell3DMeasurements segmenttation, classification of migration phenotypes, calculation of cell specific and spheroid specific parameters B5_20x_medium_IgG_good settings_Analysis.tar | ||
| C4_20x_medium_YAP Appendix II Microscopy Scanning confocal microscopy PLOSTHES http://localhost/plosthes.2017-1#10559 single time point 24 h Ch1: YAP-AlexaFluor488, Ch2: Phalloidin-AlexaFluor633, Ch3: DAPI, Ch4: reflection, Ch5: transmission Zeiss Plan-Apochromat 20x/0.8NA 0.8 C4_20x_medium_YAP_Raw.tar 1.2 �m 1.2 �m 2 �m https://github.com/Mverp/Cell3DMeasurements segmenttation, classification of migration phenotypes, calculation of cell specific and spheroid specific parameters C4_20x_medium_YAP_Analysis.tar | ||
| C7_20x_medium_YAP Appendix II Microscopy Scanning confocal microscopy PLOSTHES http://localhost/plosthes.2017-1#10559 single time point 24 h Ch1: YAP-AlexaFluor488, Ch2: Phalloidin-AlexaFluor633, Ch3: DAPI, Ch4: reflection, Ch5: transmission Zeiss Plan-Apochromat 20x/0.8NA 0.8 C7_20x_medium_YAP_Raw.tar 1.2 �m 1.2 �m 2 �m https://github.com/Mverp/Cell3DMeasurements segmenttation, classification of migration phenotypes, calculation of cell specific and spheroid specific parameters C7_20x_medium_YAP_Analysis.tar | ||
| E2_20x_medium_YAP Appendix II Microscopy Scanning confocal microscopy PLOSTHES http://localhost/plosthes.2017-1#10559 single time point 24 h Ch1: YAP-AlexaFluor488, Ch2: Phalloidin-AlexaFluor633, Ch3: DAPI, Ch4: reflection, Ch5: transmission Zeiss Plan-Apochromat 20x/0.8NA 0.8 E2_20x_medium_YAP_Raw.tar 1.2 �m 1.2 �m 2 �m https://github.com/Mverp/Cell3DMeasurements segmenttation, classification of migration phenotypes, calculation of cell specific and spheroid specific parameters E2_20x_medium_YAP_Analysis.tar | ||
| F7_20x_medium_YAP Appendix II Microscopy Scanning confocal microscopy PLOSTHES http://localhost/plosthes.2017-1#10559 single time point 24 h Ch1: YAP-AlexaFluor488, Ch2: Phalloidin-AlexaFluor633, Ch3: DAPI, Ch4: reflection, Ch5: transmission Zeiss Plan-Apochromat 20x/0.8NA 0.8 F7_20x_medium_YAP_Raw.tar 1.2 �m 1.2 �m 2 �m https://github.com/Mverp/Cell3DMeasurements segmenttation, classification of migration phenotypes, calculation of cell specific and spheroid specific parameters F7_20x_medium_YAP_Analysis.tar | ||
| G6_20x_medium_IgG Appendix II Microscopy Scanning confocal microscopy PLOSTHES http://localhost/plosthes.2017-1#10559 single time point 24 h Ch1: IgG1-AlexaFluor488, Ch2: Phalloidin-AlexaFluor633, Ch3: DAPI, Ch4: reflection, Ch5: transmission Zeiss Plan-Apochromat 20x/0.8NA 0.8 G6_20x_medium_IgG_Raw.tar 1.2 �m 1.2 �m 2 �m https://github.com/Mverp/Cell3DMeasurements segmenttation, classification of migration phenotypes, calculation of cell specific and spheroid specific parameters G6_20x_medium_IgG_Analysis.tar | ||
| G9_20x_medium_YAP Appendix II Microscopy Scanning confocal microscopy PLOSTHES http://localhost/plosthes.2017-1#10559 single time point 24 h Ch1: YAP-AlexaFluor488, Ch2: Phalloidin-AlexaFluor633, Ch3: DAPI, Ch4: reflection, Ch5: transmission Zeiss Plan-Apochromat 20x/0.8NA 0.8 G9_20x_medium_YAP_Raw.tar 1.2 �m 1.2 �m 2 �m https://github.com/Mverp/Cell3DMeasurements segmenttation, classification of migration phenotypes, calculation of cell specific and spheroid specific parameters G9_20x_medium_YAP_Analysis.tar | ||
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...sa/a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N3.txt
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| Sample Name Protocol REF Parameter Value[imaging modality] Term Source REF Term Accession Number Parameter Value[imaging sequence type] Term Source REF Term Accession Number Parameter Value[observation period] Term Source REF Term Accession Number Unit Term Source REF Term Accession Number Parameter Value[channel definition] Parameter Value[objective lens] Parameter Value[numerical aperture] Raw Data File Parameter Value[PixelsizeX] Unit Term Source REF Term Accession Number Parameter Value[PixelsizeY] Unit Term Source REF Term Accession Number Parameter Value[PixelsizeZ] Unit Term Source REF Term Accession Number Protocol REF Data Transformation Name Derived Data File | ||
| B2_medium_20x_goodsettings_YAP Appendix II Microscopy Scanning confocal microscopy PLOSTHES http://localhost/plosthes.2017-1#10559 single time point 24 h Ch1: YAP-AlexaFluor488, Ch2: Phalloidin-AlexaFluor633, Ch3: DAPI, Ch4: reflection, Ch5: transmission Zeiss Plan-Apochromat 20x/0.8NA 0.8 B2_medium_20x_goodsettings_YAP_Raw.tar 1.2 �m 1.2 �m 2 �m https://github.com/Mverp/Cell3DMeasurements segmenttation, classification of migration phenotypes, calculation of cell specific and spheroid specific parameters B2_medium_20x_goodsettings_YAP_Analysis.tar | ||
| B5_medium_20x_YAP Appendix II Microscopy Scanning confocal microscopy PLOSTHES http://localhost/plosthes.2017-1#10559 single time point 24 h Ch1: YAP-AlexaFluor488, Ch2: Phalloidin-AlexaFluor633, Ch3: DAPI, Ch4: reflection, Ch5: transmission Zeiss Plan-Apochromat 20x/0.8NA 0.8 B5_medium_20x_YAP_Raw.tar 1.2 �m 1.2 �m 2 �m https://github.com/Mverp/Cell3DMeasurements segmenttation, classification of migration phenotypes, calculation of cell specific and spheroid specific parameters B5_medium_20x_YAP_Analysis.tar | ||
| C5_medium_20x_IgG Appendix II Microscopy Scanning confocal microscopy PLOSTHES http://localhost/plosthes.2017-1#10559 single time point 24 h Ch1: IgG1-AlexaFluor488, Ch2: Phalloidin-AlexaFluor633, Ch3: DAPI, Ch4: reflection, Ch5: transmission Zeiss Plan-Apochromat 20x/0.8NA 0.8 C5_medium_20x_IgG_Raw.tar 1.2 �m 1.2 �m 2 �m https://github.com/Mverp/Cell3DMeasurements segmenttation, classification of migration phenotypes, calculation of cell specific and spheroid specific parameters C5_medium_20x_IgG_Analysis.tar | ||
| D5_medium_20x_YAP Appendix II Microscopy Scanning confocal microscopy PLOSTHES http://localhost/plosthes.2017-1#10559 single time point 24 h Ch1: YAP-AlexaFluor488, Ch2: Phalloidin-AlexaFluor633, Ch3: DAPI, Ch4: reflection, Ch5: transmission Zeiss Plan-Apochromat 20x/0.8NA 0.8 D5_medium_20x_YAP_Raw.tar 1.2 �m 1.2 �m 2 �m https://github.com/Mverp/Cell3DMeasurements segmenttation, classification of migration phenotypes, calculation of cell specific and spheroid specific parameters D5_medium_20x_YAP_Analysis.tar | ||
| E5_medium_20x_YAP Appendix II Microscopy Scanning confocal microscopy PLOSTHES http://localhost/plosthes.2017-1#10559 single time point 24 h Ch1: YAP-AlexaFluor488, Ch2: Phalloidin-AlexaFluor633, Ch3: DAPI, Ch4: reflection, Ch5: transmission Zeiss Plan-Apochromat 20x/0.8NA 0.8 E5_medium_20x_YAP_Raw.tar 1.2 �m 1.2 �m 2 �m https://github.com/Mverp/Cell3DMeasurements segmenttation, classification of migration phenotypes, calculation of cell specific and spheroid specific parameters E5_medium_20x_YAP_Analysis.tar | ||
| F2_medium_20x_YAP Appendix II Microscopy Scanning confocal microscopy PLOSTHES http://localhost/plosthes.2017-1#10559 single time point 24 h Ch1: YAP-AlexaFluor488, Ch2: Phalloidin-AlexaFluor633, Ch3: DAPI, Ch4: reflection, Ch5: transmission Zeiss Plan-Apochromat 20x/0.8NA 0.8 F2_medium_20x_YAP_Raw.tar 1.2 �m 1.2 �m 2 �m https://github.com/Mverp/Cell3DMeasurements segmenttation, classification of migration phenotypes, calculation of cell specific and spheroid specific parameters F2_medium_20x_YAP_Analysis.tar | ||
| F5_medium_20x_YAP Appendix II Microscopy Scanning confocal microscopy PLOSTHES http://localhost/plosthes.2017-1#10559 single time point 24 h Ch1: YAP-AlexaFluor488, Ch2: Phalloidin-AlexaFluor633, Ch3: DAPI, Ch4: reflection, Ch5: transmission Zeiss Plan-Apochromat 20x/0.8NA 0.8 F5_medium_20x_YAP_Raw.tar 1.2 �m 1.2 �m 2 �m https://github.com/Mverp/Cell3DMeasurements segmenttation, classification of migration phenotypes, calculation of cell specific and spheroid specific parameters F5_medium_20x_YAP_Analysis.tar | ||
| G2_medium_20x_YAP Appendix II Microscopy Scanning confocal microscopy PLOSTHES http://localhost/plosthes.2017-1#10559 single time point 24 h Ch1: YAP-AlexaFluor488, Ch2: Phalloidin-AlexaFluor633, Ch3: DAPI, Ch4: reflection, Ch5: transmission Zeiss Plan-Apochromat 20x/0.8NA 0.8 G2_medium_20x_YAP_Raw.tar 1.2 �m 1.2 �m 2 �m https://github.com/Mverp/Cell3DMeasurements segmenttation, classification of migration phenotypes, calculation of cell specific and spheroid specific parameters G2_medium_20x_YAP_Analysis.tar | ||
| G5_medium_20x_YAP Appendix II Microscopy Scanning confocal microscopy PLOSTHES http://localhost/plosthes.2017-1#10559 single time point 24 h Ch1: YAP-AlexaFluor488, Ch2: Phalloidin-AlexaFluor633, Ch3: DAPI, Ch4: reflection, Ch5: transmission Zeiss Plan-Apochromat 20x/0.8NA 0.8 G5_medium_20x_YAP_Raw.tar 1.2 �m 1.2 �m 2 �m https://github.com/Mverp/Cell3DMeasurements segmenttation, classification of migration phenotypes, calculation of cell specific and spheroid specific parameters G5_medium_20x_YAP_Analysis.tar |
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...sa/a_2018_3dsphinvasion_ht1080_collagen_spheroid_invasion_assay_microscopy_imaging-N4.txt
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| Sample Name Protocol REF Parameter Value[imaging modality] Term Source REF Term Accession Number Parameter Value[imaging sequence type] Term Source REF Term Accession Number Parameter Value[observation period] Term Source REF Term Accession Number Unit Term Source REF Term Accession Number Parameter Value[channel definition] Parameter Value[objective lens] Parameter Value[numerical aperture] Raw Data File Parameter Value[PixelsizeX] Unit Term Source REF Term Accession Number Parameter Value[PixelsizeY] Unit Term Source REF Term Accession Number Parameter Value[PixelsizeZ] Unit Term Source REF Term Accession Number Protocol REF Data Transformation Name Derived Data File | ||
| Medium_B2_20x_YAP Appendix II Microscopy Scanning confocal microscopy PLOSTHES http://localhost/plosthes.2017-1#10559 single time point 24 h Ch1: YAP-AlexaFluor488, Ch2: Phalloidin-AlexaFluor633, Ch3: DAPI, Ch4: reflection, Ch5: transmission Zeiss Plan-Apochromat 20x/0.8NA 0.8 Medium_B2_20x_YAP_Raw.tar 1.2 �m 1.2 �m 2 �m https://github.com/Mverp/Cell3DMeasurements segmenttation, classification of migration phenotypes, calculation of cell specific and spheroid specific parameters Medium_B2_20x_YAP_Analysis.tar | ||
| Medium_B5_20x_YAP Appendix II Microscopy Scanning confocal microscopy PLOSTHES http://localhost/plosthes.2017-1#10559 single time point 24 h Ch1: YAP-AlexaFluor488, Ch2: Phalloidin-AlexaFluor633, Ch3: DAPI, Ch4: reflection, Ch5: transmission Zeiss Plan-Apochromat 20x/0.8NA 0.8 Medium_B5_20x_YAP_Raw.tar 1.2 �m 1.2 �m 2 �m https://github.com/Mverp/Cell3DMeasurements segmenttation, classification of migration phenotypes, calculation of cell specific and spheroid specific parameters Medium_B5_20x_YAP_Analysis.tar | ||
| Medium_C2_20x_YAP Appendix II Microscopy Scanning confocal microscopy PLOSTHES http://localhost/plosthes.2017-1#10559 single time point 24 h Ch1: YAP-AlexaFluor488, Ch2: Phalloidin-AlexaFluor633, Ch3: DAPI, Ch4: reflection, Ch5: transmission Zeiss Plan-Apochromat 20x/0.8NA 0.8 Medium_C2_20x_YAP_Raw.tar 1.2 �m 1.2 �m 2 �m https://github.com/Mverp/Cell3DMeasurements segmenttation, classification of migration phenotypes, calculation of cell specific and spheroid specific parameters Medium_C2_20x_YAP_Analysis.tar | ||
| Medium_C5_20x_YAP Appendix II Microscopy Scanning confocal microscopy PLOSTHES http://localhost/plosthes.2017-1#10559 single time point 24 h Ch1: YAP-AlexaFluor488, Ch2: Phalloidin-AlexaFluor633, Ch3: DAPI, Ch4: reflection, Ch5: transmission Zeiss Plan-Apochromat 20x/0.8NA 0.8 Medium_C5_20x_YAP_Raw.tar 1.2 �m 1.2 �m 2 �m https://github.com/Mverp/Cell3DMeasurements segmenttation, classification of migration phenotypes, calculation of cell specific and spheroid specific parameters Medium_C5_20x_YAP_Analysis.tar | ||
| Medium_D2_20x_YAP Appendix II Microscopy Scanning confocal microscopy PLOSTHES http://localhost/plosthes.2017-1#10559 single time point 24 h Ch1: YAP-AlexaFluor488, Ch2: Phalloidin-AlexaFluor633, Ch3: DAPI, Ch4: reflection, Ch5: transmission Zeiss Plan-Apochromat 20x/0.8NA 0.8 Medium_D2_20x_YAP_Raw.tar 1.2 �m 1.2 �m 2 �m https://github.com/Mverp/Cell3DMeasurements segmenttation, classification of migration phenotypes, calculation of cell specific and spheroid specific parameters Medium_D2_20x_YAP_Analysis.tar | ||
| Medium_D5_20x_IgG Appendix II Microscopy Scanning confocal microscopy PLOSTHES http://localhost/plosthes.2017-1#10559 single time point 24 h Ch1: IgG1-AlexaFluor488, Ch2: Phalloidin-AlexaFluor633, Ch3: DAPI, Ch4: reflection, Ch5: transmission Zeiss Plan-Apochromat 20x/0.8NA 0.8 Medium_D5_20x_IgG_Raw.tar 1.2 �m 1.2 �m 2 �m https://github.com/Mverp/Cell3DMeasurements segmenttation, classification of migration phenotypes, calculation of cell specific and spheroid specific parameters Medium_D5_20x_IgG_Analysis.tar | ||
| Medium_E2_20x_YAP 10 Appendix II Microscopy Scanning confocal microscopy PLOSTHES http://localhost/plosthes.2017-1#10559 single time point 24 h Ch1: YAP-AlexaFluor488, Ch2: Phalloidin-AlexaFluor633, Ch3: DAPI, Ch4: reflection, Ch5: transmission Zeiss Plan-Apochromat 20x/0.8NA 0.8 Medium_E2_20x_YAP 10_Raw.tar 1.2 �m 1.2 �m 2 �m https://github.com/Mverp/Cell3DMeasurements segmenttation, classification of migration phenotypes, calculation of cell specific and spheroid specific parameters Medium_E2_20x_YAP 10_Analysis.tar | ||
| Medium_E5_20x_YAP 10 Appendix II Microscopy Scanning confocal microscopy PLOSTHES http://localhost/plosthes.2017-1#10559 single time point 24 h Ch1: YAP-AlexaFluor488, Ch2: Phalloidin-AlexaFluor633, Ch3: DAPI, Ch4: reflection, Ch5: transmission Zeiss Plan-Apochromat 20x/0.8NA 0.8 Medium_E5_20x_YAP 10_Raw.tar 1.2 �m 1.2 �m 2 �m https://github.com/Mverp/Cell3DMeasurements segmenttation, classification of migration phenotypes, calculation of cell specific and spheroid specific parameters Medium_E5_20x_YAP 10_Analysis.tar | ||
| Medium_F2_20x_YAP 10 Appendix II Microscopy Scanning confocal microscopy PLOSTHES http://localhost/plosthes.2017-1#10559 single time point 24 h Ch1: YAP-AlexaFluor488, Ch2: Phalloidin-AlexaFluor633, Ch3: DAPI, Ch4: reflection, Ch5: transmission Zeiss Plan-Apochromat 20x/0.8NA 0.8 Medium_F2_20x_YAP 10_Raw.tar 1.2 �m 1.2 �m 2 �m https://github.com/Mverp/Cell3DMeasurements segmenttation, classification of migration phenotypes, calculation of cell specific and spheroid specific parameters Medium_F2_20x_YAP 10_Analysis.tar | ||
| Medium_G2_20x_YAP 10 Appendix II Microscopy Scanning confocal microscopy PLOSTHES http://localhost/plosthes.2017-1#10559 single time point 24 h Ch1: YAP-AlexaFluor488, Ch2: Phalloidin-AlexaFluor633, Ch3: DAPI, Ch4: reflection, Ch5: transmission Zeiss Plan-Apochromat 20x/0.8NA 0.8 Medium_G2_20x_YAP 10_Raw.tar 1.2 �m 1.2 �m 2 �m https://github.com/Mverp/Cell3DMeasurements segmenttation, classification of migration phenotypes, calculation of cell specific and spheroid specific parameters Medium_G2_20x_YAP 10_Analysis.tar | ||
| Medium_G5_20x_YAP 10 Appendix II Microscopy Scanning confocal microscopy PLOSTHES http://localhost/plosthes.2017-1#10559 single time point 24 h Ch1: YAP-AlexaFluor488, Ch2: Phalloidin-AlexaFluor633, Ch3: DAPI, Ch4: reflection, Ch5: transmission Zeiss Plan-Apochromat 20x/0.8NA 0.8 Medium_G5_20x_YAP 10_Raw.tar 1.2 �m 1.2 �m 2 �m https://github.com/Mverp/Cell3DMeasurements segmenttation, classification of migration phenotypes, calculation of cell specific and spheroid specific parameters Medium_G5_20x_YAP 10_Analysis.tar |
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@gerritsmedia It seems that this ISA Assay File is missing an "Assay Name" (and values) right before the "Raw Data File" Field. The Field is required to pass ISA syntactic validation.
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I checked it with the Isacreator and indeed it seems that I deleted this particular column. I thought, the assay name is already in the filename itself, why repeat it? But, I can add it again.
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That column refers to the specific assay execution/application, while the assay filename is the name of the assay table, containing the details of all the specific assay application. Could you please to add the column back in for this PR?
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Some "Assay Name" may have multiple output files hence the field. in your case, it seems indeed somehow duplicating information but it is necessary for it to be present.
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Alright, I put it back in. I've send it to Alejandra's email for the moment.
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Thanks @gerritsmedia - feel free to update your repository and the pull request. There are also issues with the protocols and parameter names (e.g. (micro)environment). The
Protocol REFcolumn refers to the protocols defined in the investigation file and the parameters have to match. To link to the documents describing the protocols, it would be better to use theStudy Protocol URIif possible.There was a problem hiding this comment.
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Some of the syntactic issues: the protocol "Appendix I" was missing the following parameters
"cell culture CO2 partial pressure;cell culture temperature;cell culture antibiotics;cell culture serum concentration;cell culture serum;cell culture medium;cell culture vessel;(micro)environment"
The protocol "Appendix II Microscopy" was defined as "Appendix II Microscopy.pdf" in the investigation file and they need to match in investigation and study files.
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I will update the files and change the protocol names to *.pdf to make it consistent over the dataset. For the rest, the parameters mentioned above (for appendix I) are all included, however, not with the exact terms. Do I need to include these terms literally? In that case, I need to make some slight adaptations to the protocol in the way it is written.
What do you mean with (micro)environment? I could adapt the section 'Spheroid embedding in 3D collagen', such that it includes the term '(micro)environment' literally. Could I freely specify the (micro)environment as 'reconstituted fibrillar rattail collagen', or is there a standard term to specify the (micro)environment?
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Hi, I updated the files, except for the protocol, I will work on that later. Are the isa tab files correct now?
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The file Appendix I 3D spheroid culture.pdf is also updated now.