cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.6591396
title: Morse Decoder

description: This repo provides the python code (jupyter notebook) for the Morse Decoder, which is used to convert the data to Morse code and then letters.
DOI: 10.5281/zenodo.6591409
title: Mulberry Disasters in Chinese Local Gazetteers

description: This dataset contains 404 mulberry disasters found in a digital collection of 4,000 Chinese local gazetteers (published in Erudition's Zhongguo Fangzhi Ku, or the Database of Chinese Local Gazetteers) that was curated during 2018 and 2019 by scholars at the Max Planck Institute for the History of Science to support their joint research paper entitled: “What Is Local Knowledge: Digital Humanities and Yuan Dynasty Disasters in Imperial China’s Local Gazetteers.” The paper appeared in the <em>Journal of Chinese History</em> in its 2020 spring issue. The authors use this dataset to ask what results the emerging methodology of analyzing data drawn from historical sources can produce for historical research, given that such data-driven analysis is inevitably quantitative and that many historians believe this would contradict the core value of studies in the humanities. This dataset is accompanied by a data paper to be published by Brill's Digital Concordances Platform. In the data paper, the authors give information about the full curation cycle of this dataset, including the research goal that motivated the curation, the sources that were used, and the curation/cleansing/preparation process. The authors also explain this dataset in detail, including the kind of information it contains and its overall temporal and geospatial distributions. In conclusion, they discuss the potential usages of the dataset. With this paper, we also hope to offer an exemplary data curation workflow for collecting data from historical sources that includes not only data curation (whether manual or semiautomatic), but also the practical steps of data cleansing and normalization that reflect the various historical considerations in the process.
DOI: 10.5281/zenodo.6591408
title: Mulberry Disasters in Chinese Local Gazetteers

description: This dataset contains 404 mulberry disasters found in a digital collection of 4,000 Chinese local gazetteers (published in Erudition's Zhongguo Fangzhi Ku, or the Database of Chinese Local Gazetteers) that was curated during 2018 and 2019 by scholars at the Max Planck Institute for the History of Science to support their joint research paper entitled: “What Is Local Knowledge: Digital Humanities and Yuan Dynasty Disasters in Imperial China’s Local Gazetteers.” The paper appeared in the <em>Journal of Chinese History</em> in its 2020 spring issue. The authors use this dataset to ask what results the emerging methodology of analyzing data drawn from historical sources can produce for historical research, given that such data-driven analysis is inevitably quantitative and that many historians believe this would contradict the core value of studies in the humanities. This dataset is accompanied by a data paper to be published by Brill's Digital Concordances Platform. In the data paper, the authors give information about the full curation cycle of this dataset, including the research goal that motivated the curation, the sources that were used, and the curation/cleansing/preparation process. The authors also explain this dataset in detail, including the kind of information it contains and its overall temporal and geospatial distributions. In conclusion, they discuss the potential usages of the dataset. With this paper, we also hope to offer an exemplary data curation workflow for collecting data from historical sources that includes not only data curation (whether manual or semiautomatic), but also the practical steps of data cleansing and normalization that reflect the various historical considerations in the process.
DOI: 10.5281/zenodo.6591369
title: Example dataset for Tracking Metrics using TrackMate and Oneat

description: In this dataset we compare the automated tracking results using the standard TrackMate algorithms for frame to frame and segment to segment linking with the ground truth dataset. Furthermore we use Oneat to correct the branches of the lineage trees and using oneat as TrackCorrector we recompute the metrics to show improvements over TrackMate track linking algorithms. Tracking Metrics Simple LAP tracker + Oneat {DET : 0.9964, CT : 0.73531, TRA : 0.9933, TF : 0.97518, BCi : 0.10526} LAP Tracker with track splitting and Quality as additional cost {DET : 0.9900, CT : 0.677033, TRA : 0.986785; TF : 0.95041, BCi : 0.04347} LAP Tracker with track splitting and Quality as additional cost + Oneat {DET : 0.98911, CT : 0.672629, TRA : 0.985774, TF : 0.948692, BCi : 0.05555} LAP Tracker without track splitting and Quality as additional cost + Oneat {DET : 0.990083, CT : 0.6766, TRA : 0.986742, TF : 0.9521, BCi 0.054}
description: Computational support provided by Jean Zay dynamic access grant: AD011013396, oneat model training and evaluation was performed on Jean Zay compute nodes
DOI: 10.34808/gjv5-qj02
title: High grade serous carcinoma - Female, 66 - Tissue image [5290730025529521]

description: This is the histopathological image of OVARY tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 1000 slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 66Clinical description: Tumor of right ovary.Gender: FemaleDiagnosis:Classification: ICD-O_3.2Classification code: CYSTIC, MUCINOUS AND SEROUS NEOPLASMSDiagnosis: High grade serous carcinomaResult of the histopathological examination: High grade serous carcinoma of ovary: CK7+, PAX8+, WT1+, ER+, CK17-, CK20-, SATB2-, CDX2-.Sample:Material: FFPECollecting method: Surgical specimenTopography: FEMALE GENITAL ORGANSOrgan: OVARYTissue: OvaryType of staining: positive/IHCStaining: Not applicableAntibody: ERTechnology:Equipment: Pannoramic 1000Lens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/w0vz-8202
title: Mucinous adenocarcinoma - Female, 68 - Tissue image [5290730025519451]

description: This is the histopathological image of COLON tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 1000 slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 68Clinical description: Suspicion of appendicitis.Gender: FemaleDiagnosis:Classification: ICD-O_3.2Classification code: CYSTIC, MUCINOUS AND SEROUS NEOPLASMSDiagnosis: Mucinous adenocarcinomaResult of the histopathological examination: Mucinous adenocarcinoma of appendix (G3).Sample:Material: FFPECollecting method: Surgical specimenTopography: DIGESTIVE ORGANSOrgan: COLONTissue: AppendixType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 1000Lens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/mn23-ts92
title: Endometrioid carcinoma, NOS - Female, 78 - Tissue image [5290730025529041]

description: This is the histopathological image of CORPUS UTERI tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 1000 slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 78Clinical description: Tumor of uterine cavity.Gender: FemaleDiagnosis:Classification: ICD-O_3.2Classification code: ADENOMAS AND ADENOCARCINOMASDiagnosis: Endometrioid carcinoma, NOSResult of the histopathological examination: Endometrioid endometrial adenocarcinoma G1.Sample:Material: FFPECollecting method: Surgical specimenTopography: FEMALE GENITAL ORGANSOrgan: CORPUS UTERITissue: EndometriumType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 1000Lens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/x6wj-ne97
title: Nontoxic multinodular goitre - Female, 54 - Tissue image [5290730025528241]

description: This is the histopathological image of THYROID GLAND tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 1000 slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 54Clinical description: Enlarged thyroid gland.Gender: FemaleDiagnosis:Classification: ICD-10_10-20Classification code: Chapter IV - Endocrine, nutritional and metabolic diseasesDiagnosis: Nontoxic multinodular goitreResult of the histopathological examination: Multinodular goitre (with cysts and calcifications).Sample:Material: FFPECollecting method: Surgical specimenTopography: THYROID AND OTHER ENDOCRINE GLANDSOrgan: THYROID GLANDTissue: Thyroid glandType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 1000Lens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/9vc0-8f83
title: Cervical intraepithelial neoplasia, grade III - Female, 74 - Tissue image [5290730025527111]

description: This is the histopathological image of CERVIX UTERI tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 1000 slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 74Clinical description: No clinical data.Gender: FemaleDiagnosis:Classification: ICD-O_3.2Classification code: SQUAMOUS CELL NEOPLASMSDiagnosis: Cervical intraepithelial neoplasia, grade IIIResult of the histopathological examination: Cervical intraepithelial neoplasia, grade III (CINIII/HSIL).Sample:Material: FFPECollecting method: Excision of lesionsTopography: FEMALE GENITAL ORGANSOrgan: CERVIX UTERITissue: ExocervixType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 1000Lens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/k4cy-8n44
title: Hypertrophy of breast - Male, 21 - Tissue image [5290730025528021]

description: This is the histopathological image of BREAST tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 1000 slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 21Clinical description: Enlarged right breast.Gender: MaleDiagnosis:Classification: ICD-10_10-20Classification code: Chapter XIV - Diseases of the genitourinary systemDiagnosis: Hypertrophy of breastResult of the histopathological examination: Gynecomastia.Sample:Material: FFPECollecting method: Surgical specimenTopography: BREASTOrgan: BREASTTissue: Breast, NOSType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 1000Lens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/vyfj-yf24
title: LYMPH NODES, Obturator lymph node - Female, 60 - Tissue image [5290730025508211]

description: This is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 60Clinical description: Polyp of the endometrium.Gender: FemaleDiagnosis:Classification: HealthyClassification code: Diagnosis: Result of the histopathological examination: The lymph node is free of metastasis.Sample:Material: FFPECollecting method: Surgical specimenTopography: LYMPH NODESOrgan: LYMPH NODESTissue: Obturator lymph nodeType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/1vxn-ct44
title: Squamous cell carcinoma, nonkeratinizing, NOS - Female, 43 - Tissue image [5290730025512191]

description: This is the histopathological image of CERVIX UTERI tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 1000 slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 43Clinical description: No clinical data.Gender: FemaleDiagnosis:Classification: ICD-O_3.2Classification code: SQUAMOUS CELL NEOPLASMSDiagnosis: Squamous cell carcinoma, nonkeratinizing, NOSResult of the histopathological examination: Squamous cell carcinoma, non-keratinizing type G3.Sample:Material: FFPECollecting method: Surgical biopsyTopography: FEMALE GENITAL ORGANSOrgan: CERVIX UTERITissue: ExocervixType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 1000Lens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/2mxd-wa81
title: High grade serous carcinoma - Female, 66 - Tissue image [5290730025527621]

description: This is the histopathological image of OVARY tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 1000 slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 66Clinical description: Tumor of right ovary.Gender: FemaleDiagnosis:Classification: ICD-O_3.2Classification code: CYSTIC, MUCINOUS AND SEROUS NEOPLASMSDiagnosis: High grade serous carcinomaResult of the histopathological examination: High grade serous carcinoma of ovary: CK7+, PAX8+, WT1+, ER+, CK17-, CK20-, SATB2-, CDX2-.Sample:Material: FFPECollecting method: Surgical specimenTopography: FEMALE GENITAL ORGANSOrgan: OVARYTissue: OvaryType of staining: positive/IHCStaining: Not applicableAntibody: SATB2Technology:Equipment: Pannoramic 1000Lens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/tnrr-eb78
title: Mucinous adenocarcinoma - Female, 68 - Tissue image [5290730025511481]

description: This is the histopathological image of COLON tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 1000 slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 68Clinical description: Suspicion of appendicitis.Gender: FemaleDiagnosis:Classification: ICD-O_3.2Classification code: CYSTIC, MUCINOUS AND SEROUS NEOPLASMSDiagnosis: Mucinous adenocarcinomaResult of the histopathological examination: Mucinous adenocarcinoma of appendix (G3).Sample:Material: FFPECollecting method: Surgical specimenTopography: DIGESTIVE ORGANSOrgan: COLONTissue: AppendixType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 1000Lens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/mg7g-ns87
title: Angiomyolipoma - Female, 80 - Tissue image [5290730025503351]

description: This is the histopathological image of KIDNEY tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 1000 slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 80Clinical description: 2,5 x 3,0 x 2,5 cm tumor of left kidney.Gender: FemaleDiagnosis:Classification: ICD-O_3.2Classification code: LIPOMATOUS NEOPLASMSDiagnosis: AngiomyolipomaResult of the histopathological examination: Angiomyolipoma nerki: SMA+, HMB45 focally+, MelanA focally+, S100+, ER-, CD117-, CKAE1/AE3-, PAX8-, Ki-67 1%.Sample:Material: FFPECollecting method: Surgical specimenTopography: URINARY TRACTOrgan: KIDNEYTissue: Kidney, NOSType of staining: positive/IHCStaining: Not applicableAntibody: Ki-67Technology:Equipment: Pannoramic 1000Lens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/4mda-4z16
title: LYMPH NODES, Obturator lymph node - Female, 60 - Tissue image [5290730025508141]

description: This is the histopathological image of LYMPH NODES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 250 3DHistech slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 60Clinical description: Polyp of the endometrium.Gender: FemaleDiagnosis:Classification: HealthyClassification code: Diagnosis: Result of the histopathological examination: The lymph node is free of metastasis.Sample:Material: FFPECollecting method: Surgical specimenTopography: LYMPH NODESOrgan: LYMPH NODESTissue: Obturator lymph nodeType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 250 3DHistechLens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/pnsa-c564
title: Squamous intraepithelial neoplasia, grade III - Female, 45 - Tissue image [5290730025514291]

description: This is the histopathological image of CORPUS UTERI tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 1000 slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 45Clinical description: No clinical data.Gender: FemaleDiagnosis:Classification: ICD-O_3.2Classification code: SQUAMOUS CELL NEOPLASMSDiagnosis: Squamous intraepithelial neoplasia, grade IIIResult of the histopathological examination: Squamous intraepithelial neoplasia (intermediate and high grade, CINII/CINIII, HSIL): p16+, HPV-Ab-, Ki-67 increased proliferation index.Sample:Material: FFPECollecting method: ScrapingsTopography: FEMALE GENITAL ORGANSOrgan: CORPUS UTERITissue: EndometriumType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 1000Lens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/rcpz-5z81
title: Nontoxic multinodular goitre - Female, 41 - Tissue image [52907300255211]

description: This is the histopathological image of THYROID GLAND tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 1000 slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 41Clinical description: Numerous nodules of thyroid gland.Gender: FemaleDiagnosis:Classification: ICD-10_10-20Classification code: Chapter IV - Endocrine, nutritional and metabolic diseasesDiagnosis: Nontoxic multinodular goitreResult of the histopathological examination: Multinodular goitre.Sample:Material: FFPECollecting method: Surgical specimenTopography: THYROID AND OTHER ENDOCRINE GLANDSOrgan: THYROID GLANDTissue: Thyroid glandType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 1000Lens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/s9z0-g224
title: Ancient schwannoma - Female, 57 - Tissue image [5290730025522461]

description: This is the histopathological image of OTHER AND ILL-DEFINED SITES tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 1000 slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 57Clinical description: Tumor of left axilla.Gender: FemaleDiagnosis:Classification: ICD-O_3.2Classification code: NERVE SHEATH TUMORSDiagnosis: Ancient schwannomaResult of the histopathological examination: Ancient schwannoma: S100+, SOX10+, CD68 focally+, CD56 focally+, CD34 single cells +, CKAE1/AE3-, SMA-, DES-, MelanA-, Ki-67 5%.Sample:Material: FFPECollecting method: Excision of lesionsTopography: OTHER AND ILL-DEFINED SITESOrgan: OTHER AND ILL-DEFINED SITESTissue: Axilla, NOSType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 1000Lens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/k8d6-gs30
title: Neuroendocrine tumor, grade 1 - Male, 56 - Tissue image [5290730025515171]

description: This is the histopathological image of SMALL INTESTINE tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 1000 slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 56Clinical description: CT: 41 x 20 x 31 mm tumor of duodenum.Gender: MaleDiagnosis:Classification: ICD-O_3.2Classification code: ADENOMAS AND ADENOCARCINOMASDiagnosis: Neuroendocrine tumor, grade 1Result of the histopathological examination: Neuroendocrine tumor of pancreas (NET G1): CHR+, SYN+, CKAE1/AE3+, CK7 + (perinuclear dot), CK20-, Ki-67 1%. 1 mitosis/2 mm2.Sample:Material: FFPECollecting method: Surgical specimenTopography: DIGESTIVE ORGANSOrgan: SMALL INTESTINETissue: DuodenumType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 1000Lens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/4v8w-pc77
title: Nontoxic multinodular goitre - Female, 54 - Tissue image [5290730025522921]

description: This is the histopathological image of THYROID GLAND tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 1000 slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 54Clinical description: Enlarged thyroid gland.Gender: FemaleDiagnosis:Classification: ICD-10_10-20Classification code: Chapter IV - Endocrine, nutritional and metabolic diseasesDiagnosis: Nontoxic multinodular goitreResult of the histopathological examination: Multinodular goitre (with cysts and calcifications).Sample:Material: FFPECollecting method: Surgical specimenTopography: THYROID AND OTHER ENDOCRINE GLANDSOrgan: THYROID GLANDTissue: Thyroid glandType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 1000Lens: 20xOrganization:Source: Medical University Gdańsk
DOI: 10.34808/256z-eh38
title: Endometrioid carcinoma, NOS - Female, 78 - Tissue image [5290730025522131]

description: This is the histopathological image of CORPUS UTERI tissue sample obtained in Medical University Gdańsk and deposited in ZMDL-GUMED. The sample image was taken using: Pannoramic 1000 slide scanner (20x magnification) and saved to DICOM format. The detailed information about the patient, sample, and diagnosis are as follows: Patient:Age: 78Clinical description: Tumor of uterine cavity.Gender: FemaleDiagnosis:Classification: ICD-O_3.2Classification code: ADENOMAS AND ADENOCARCINOMASDiagnosis: Endometrioid carcinoma, NOSResult of the histopathological examination: Endometrioid endometrial adenocarcinoma G1.Sample:Material: FFPECollecting method: Surgical specimenTopography: FEMALE GENITAL ORGANSOrgan: CORPUS UTERITissue: EndometriumType of staining: positive/HEStaining: Not applicableAntibody: Not applicableTechnology:Equipment: Pannoramic 1000Lens: 20xOrganization:Source: Medical University Gdańsk