Dataset of ptychographic X-ray computed tomography of inverse opal photonic crystals produced by atomic layer deposition.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30519618", "kind": "science-record", "revision": 4, "content_hash": "sha256:d7bf49d276d121d1fdd56f3e67ab6bf926222b36ef4b62c372150c1eb8621749", "created_at": "2026-11-01T15:40:39Z", "updated_at": "2026-11-01T21:21:48Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Dataset of ptychographic X-ray computed tomography of inverse opal photonic crystals produced by atomic layer deposition.", "doi": "10.1016/j.dib.2018.10.076", "pmid": "30519618", "authors": ["Kaline P Furlan", "Emanuel Larsson", "Ana Diaz", "Mirko Holler", "Tobias Krekeler", "Martin Ritter", "Alexander Yu Petrov", "Manfred Eich", "Robert Blick", "Gerold A Schneider", "Imke Greving", "Robert Zierold", "Rolf Janßen"], "journal": "Data in brief", "year": 2018, "abstract": "This data article describes the detailed parameters for synthesizing mullite inverse opal photonic crystals via Atomic Layer Deposition (ALD), as well as the detailed image analysis routine used to interpret the data obtained by the measurement of such photonic crystals, before and after the heat treatment, via Ptychographic X-ray Computed Tomography (PXCT). The data presented in this article are related to the research article by Furlan and co-authors entitled \"Photonic materials for high-temperature applications: Synthesis and characterization by X-ray ptychographic tomography\" (Furlan et al., 2018). The data include detailed information about the ALD super-cycle process to generate the ternary oxides inside a photonic crystal template, the raw data from supporting characterization techniques, as well as the full dataset obtained from PXCT. All the data herein described is publicly available in a Mendeley Data archive \"Dataset of synthesis and characterization by PXCT of ALD-based mullite inverse opal photonic crystals\" located at https://data.mendeley.com/datasets/zn49dsk7x6/1 for any academic, educational, or research purposes.", "claims": [{"id": "claim-method", "statement": "A test for finding the Representative Volume of Interest (RVI-test) was performed by plotting the Volume Percentage (Vol. Perc.) of the void part (macro and nano pores) as a function of the volume of interest (VOI)-size, as shown in Fig. 3.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30519618", "locator": "sections[8] \"Image post processing and analysis\" paragraph 3", "quote": "A test for finding the Representative Volume of Interest (RVI-test) was performed by plotting the Volume Percentage (Vol. Perc.) of the void part (macro and nano pores) as a function of the volume of interest (VOI)-size, as shown in Fig. 3."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All the data herein described is publicly available in a Mendeley Data archive “Dataset of synthesis and characterization by PXCT of ALD-based mullite inverse opal photonic crystals” located at https://data.mendeley.com/datasets/zn49dsk7x6/1 for any academic, educational, or research purposes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30519618", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "All the data herein described is publicly available in a Mendeley Data archive “Dataset of synthesis and characterization by PXCT of ALD-based mullite inverse opal photonic crystals” located at https://data.mendeley.com/datasets/zn49dsk7x6/1 for any academic, educational, or research purposes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:30519618"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30519618", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2018.10.076", "sha256": "sha256:ff884a69bcf5c702963f835b5f4175c22cf4bae63be1d59fbe467b51f3de664a", "bytes": 23497, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2018.10.076", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6260412", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:30519618:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:54557cbe9de1faca55717dd6080161be25f4aafa329318d46388c8faf8d3060f", "bytes": 2745, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0010", "version": null, "note": null, "structure": {"pmcid": "PMC6260412", "section_index": 1, "section_title": "p", "row_count": 13, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Subject area", "Materials Science"], ["More specific subject area", "Ceramics and Composite; Nanotechnology; Surfaces, Coatings and Films"], ["Type of data", "Table, image, text file, graph, figure"], ["How data was acquired", "a.Scanning electron microscopy (SEM, Zeiss Supra 55 VP);b.Focused ion beam microscopy (FIB, FEI Helios Nanolab G3 UC);c.Ptychographic X-ray computed tomography (cSAXS beamline - Swiss Light Source, Paul Scherrer Institut, 90 K, 6.2 keV photon energy, 800 projections, 0–180° angle)d.3D rendering images (2D reconstructed and processed slices were rendered using VG Studio MAX Software, Volume Graphics)e.Grazing incidence X-ray diffraction (Bruker AXS D8 Advance, Cu Kα, 40 kV, 40 mA, step size 0.01°, step time 5 s, incident glancing angle 1.5°);f.Specular reflectance (UV–vis-NIR spectrometer, Perkin-Elmer, Lambda 1050)."], ["Data format", "Raw: Ptychographic X-ray Computed Tomography slices (*.TIF); Reflectance measurements (*.SP-datei, *.CSV); X-ray diffraction (*.RAW); SEM (*.TIF)"], ["Processed: Ptychographic X-ray Computed Tomography data – Re-sliced slices (*.TIF)"], ["Analyzed: text file, graphs and figures (*.TIF and *.DOCX)"], ["", "True metadata: text files (*.TXT) containing information about the the pixel size in the tomography raw-slices, and the conversion from tiff values to refractive index and electron density"], ["Experimental factors", "Samples, Self-assembly conditions, Atomic layer deposition process parameters, heat treatment conditions"], ["Experimental features", "Parameters for the synthesis of oxide-based ceramic inverse opal photonic crystals by Atomic Layer Deposition and characterization of the synthesized specimens by Ptychographic X-ray Computed Tomography comprising an post-measurement image analysis routine"], ["Data source location", "Hamburg, Germany, latitude 53.4603824 longitude 9.96856071271512; Hamburg, Germany, latitude 53.57492275 longitude 9.885808585389755; Villigen, Switzerland, latitude 47.5375329 longitude 8.2224404"], ["Data accessibility", "Data are presented in this article and publicly available via Mendeley Data at https://data.mendeley.com/datasets/zn49dsk7x6/draft?a=bb48c4e0-8fa7-4e9d-9028–754735b37d1f http://dx.doi.org/10.17632/zn49dsk7x6.1"], ["Related research article", "[1]K.P. Furlan, E. Larsson, A. Diaz, M. Holler, T. Krekeler, M. Ritter, A.Yu. Petrov, M. Eich, G.A. Schneider, R. Blick, I. Greving, R. Zierold, R. Janssen, Photonic materials for high-temperature applications: synthesis and characterization by X-ray ptychographic tomography, Applied Materials Today (2018) [in press]."]], "row_count": 13, "column_count": 2, "numeric_cells": 4, "header_rows": 0, "locator": "section[1]/table-wrap[1]#t0010"}}, {"id": "asset:table:pmid:30519618:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:54557cbe9de1faca55717dd6080161be25f4aafa329318d46388c8faf8d3060f", "bytes": 2745, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#t0010", "version": null, "note": null, "structure": {"pmcid": "PMC6260412", "section_index": 2, "section_title": "p", "row_count": 13, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["Subject area", "Materials Science"], ["More specific subject area", "Ceramics and Composite; Nanotechnology; Surfaces, Coatings and Films"], ["Type of data", "Table, image, text file, graph, figure"], ["How data was acquired", "a.Scanning electron microscopy (SEM, Zeiss Supra 55 VP);b.Focused ion beam microscopy (FIB, FEI Helios Nanolab G3 UC);c.Ptychographic X-ray computed tomography (cSAXS beamline - Swiss Light Source, Paul Scherrer Institut, 90 K, 6.2 keV photon energy, 800 projections, 0–180° angle)d.3D rendering images (2D reconstructed and processed slices were rendered using VG Studio MAX Software, Volume Graphics)e.Grazing incidence X-ray diffraction (Bruker AXS D8 Advance, Cu Kα, 40 kV, 40 mA, step size 0.01°, step time 5 s, incident glancing angle 1.5°);f.Specular reflectance (UV–vis-NIR spectrometer, Perkin-Elmer, Lambda 1050)."], ["Data format", "Raw: Ptychographic X-ray Computed Tomography slices (*.TIF); Reflectance measurements (*.SP-datei, *.CSV); X-ray diffraction (*.RAW); SEM (*.TIF)"], ["Processed: Ptychographic X-ray Computed Tomography data – Re-sliced slices (*.TIF)"], ["Analyzed: text file, graphs and figures (*.TIF and *.DOCX)"], ["", "True metadata: text files (*.TXT) containing information about the the pixel size in the tomography raw-slices, and the conversion from tiff values to refractive index and electron density"], ["Experimental factors", "Samples, Self-assembly conditions, Atomic layer deposition process parameters, heat treatment conditions"], ["Experimental features", "Parameters for the synthesis of oxide-based ceramic inverse opal photonic crystals by Atomic Layer Deposition and characterization of the synthesized specimens by Ptychographic X-ray Computed Tomography comprising an post-measurement image analysis routine"], ["Data source location", "Hamburg, Germany, latitude 53.4603824 longitude 9.96856071271512; Hamburg, Germany, latitude 53.57492275 longitude 9.885808585389755; Villigen, Switzerland, latitude 47.5375329 longitude 8.2224404"], ["Data accessibility", "Data are presented in this article and publicly available via Mendeley Data at https://data.mendeley.com/datasets/zn49dsk7x6/draft?a=bb48c4e0-8fa7-4e9d-9028–754735b37d1f http://dx.doi.org/10.17632/zn49dsk7x6.1"], ["Related research article", "[1]K.P. Furlan, E. Larsson, A. Diaz, M. Holler, T. Krekeler, M. Ritter, A.Yu. Petrov, M. Eich, G.A. Schneider, R. Blick, I. Greving, R. Zierold, R. Janssen, Photonic materials for high-temperature applications: synthesis and characterization by X-ray ptychographic tomography, Applied Materials Today (2018) [in press]."]], "row_count": 13, "column_count": 2, "numeric_cells": 4, "header_rows": 0, "locator": "section[1]/table-wrap[1]#t0010"}}, {"id": "asset:table:pmid:30519618:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b1d14e5188b4d88805618408e6da7f35df8a35b8722b1d8e7b43aa9435e66b70", "bytes": 862, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#t0005", "version": null, "note": "Parameters of ALD cycles.", "structure": {"pmcid": "PMC6260412", "section_index": 5, "section_title": "Low-temperature atomic layer deposition super-cycle process", "row_count": 7, "column_count": 5}, "table": {"label": "Table 1", "caption": "Parameters of ALD cycles.", "rows": [["Process", "Precursors used", "Parameters*", "Cycles"], ["#", "Description"], ["1", "Al2O3[5]", "TMA + diH2O", "0.2/60/90 + 0.05/60/90", "300"], ["2", "SiO2 type II [6]", "APTES + diH2O + O3", "2/15/45 + 0.2/15/45 + 0.05/10/30", "600"], ["3", "SiO2 type I [7], [8], [9], [10]", "TDMAS + O3", "0.05/30/30 + 0.05/10/30", "300"], ["4", "Mullite type I (combination between binary cycles #1 and #3)", "[(3DMAS + O3) × 1+ (TMA + O3) × 1) × Cycles", "(0.05/60/90 + 0.05/60/90) + (0.2/60/90 + 0.05/60/90)", "225"], ["3", "Mullite type II (combination between binary cycles #1 and #2)", "[(APTES + diH2O + O3) × 2 + (TMA + O3) × 1] × Cycles", "(2/30/120 + 0.2/30/360 + 0.05/30/90) + (0.2/30/90 + 0.05/30/120)", "150"]], "row_count": 7, "column_count": 5, "numeric_cells": 22, "header_rows": 2, "locator": "section[5]/table-wrap[1]#t0005"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Representative Volume of Interest (RVI) test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "A test for finding the Representative Volume of Interest (RVI-test) was performed by plotting the Volume Percentage (Vol. Perc.) of the void part (macro and nano pores) as a function of the volume of interest (VOI)-size, as shown in Fig. 3."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Representative Volume of Interest (RVI) test), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["All the data herein described is publicly available in a Mendeley Data archive “Dataset of synthesis and characterization by PXCT of ALD-based mullite inverse opal photonic crystals” located at https://data.mendeley.com/datasets/zn49dsk7x6/1 for any academic, educational, or research purposes."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:30519618", "asset:table:pmid:30519618:1", "asset:table:pmid:30519618:2", "asset:table:pmid:30519618:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:13:09Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 18483, "completion_tokens": 2294, "cached_tokens": 776}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:30519618", "type": "paper", "label": "pmid:30519618"}, {"id": "source:pmid:30519618", "type": "manuscript", "label": "PMID 30519618 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30519618", "type": "paper", "label": "pmid:30519618"}, {"id": "source:pmid:30519618", "type": "manuscript", "label": "PMID 30519618 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30519618", "type": "extraction", "used": ["source:pmid:30519618"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:30519618", "parent_hash": "sha256:629f603f6cedbd3d56ded589c84237918d35e6e5d36fb7e851569286ddcb292c", "fork_of": null, "generation": 3}, "gaps": ["execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"]}