Helmholtz Institute Freiberg for Resource Technology
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Codes, Models and Data for Learning locally dominant force balances in active particle systems
No full textHere, we provide all the codes, models and datasets for the submission "Learning locally dominant force balances in active particle systems"
Data publication: Numerische Untersuchung der Rayleigh-Bénard-Konvektion in einem Flüssigmetall unter dem Einfluss einer zeitlich modulierten gezeitenartigen Kraft
No full textSimulationsdaten der Dissertation: "Numerische Untersuchung der Rayleigh-Bénard-Konvektion in einem Flüssigmetall unter dem Einfluss einer zeitlich modulierten gezeitenartigen Kraft
Clinical urine microscopy for urinary tract infections
No full textUrinary tract infections (UTI) are a common disorder. Its diagnosis can be made by microscopic examination of voided urine for cellular markers of infection. We present a dataset containing 300 images and 3,562 manually annotated urinary cells labelled into seven classes of clinically significant urinary content. It is an enriched dataset with samples acquired from the unstained and untreated urine of patients with symptomatic UTI. The aim of the dataset is to facilitate UTI diagnosis in nearly all clinical settings by using a simple imaging system which leverages advanced machine learning techniques.
Data acquisition
300 urine samples were obtained from patients with symptomatic UTI between April and August 2022 from a specialist LUTS outpatient clinic in central London. Urine samples were collected as natural voids and processed on-site within one hour to mitigate cellular degradation. Brightfield microscopic examination (Olympus BX41F microscope frame, U-5RE quintuple nosepiece, U-LS30 LED illuminator, U-AC Abbe condenser) was performed at x20 objective (Olympus PLCN20x Plan C N Achromat 20x/0.4). A disposable haemocytometer (C Chip™) was used for enumeration of red cells (RBC), white cells (WBC), epithelial cells (EPC), and the presence of other cellular content per 1 µl of urine by two experienced microscopists.
Images were acquired using the aforementioned brightfield microscope using a 0.5X C-mount adapter connected to a digital colour camera (Infinity 3S-1UR, Teledyne Lumenera). Images were taken in 16-bit colour in 1392 x 1040 .tif format using Capture and Analyse software. An enriched dataset approach was taken to maximise urinary cellular content in the acquired images. Such data curation was also necessary to overcome class imbalance. Daily Kohler illumination and global white balance was performed to ensure consistency in image acquisition.
Dataset annotation
300 images were acquired and manually annotated by first identifying cells of interest as a binary semantic segmentation task. Individual pixels were dichotomously labelled as either informative cells, foreground, or non-informative background. Non-informative background was further constrained by including unidentifiable cells, such as debris or grossly out-of-focus particles. Binary annotation was initially performed using ilastik, an open-source software using a Random Forest classifier for pixel classification, then manually refined at the pixel level to ensure accurate semantic segmentation. This produced a binary mask in 1392 x 1040 .tif format for each corresponding raw colour image.
Objects of interest were then manually labelled by two expert microscopists into one of seven clinically significant multi-class categories: rods, RBC/WBC, yeast, miscellaneous, single EPC, small EPC sheet, and large EPC sheet. This produced a multi-class mask in 1392 x 1040 .tif format with a label as pixel value from 0-7, where 0 is background (Table 1).
Data structure
The dataset is organised into three root folders: img (image), bin_mask (binary mask), and mult_mask (multi-class mask). Each folder has 300 files in .tif format and labelled with an incremental number.
Table1
Folder Files Objects Count Pixel Values
img 300 Raw data 0-255
bin_mask 300 Background/Foreground 0/1
mult_mask 300 Background/Class 0
Rod 1697 1
RBC/WBC 1056 2
Yeast 41 3
Miscellaneous 550 4
Single EPC 182 5
Small EPC sheet 26 6
Large EPC sheet 10 7
Total 356
Data publication: Ion emission from warm dense matter produced by irradiation with a soft x-ray free-electron laser
No full textData set on the ion emission of different materials. Each dataset is separate and titled with the chemical symbol or abbreviation of the specific material
Data publication: Core-shell structured MCM-48-type silica-polymer hybrid material synthesis and characterization
No full textIn the current study, a core-shell structured material of MCM-48-type mesoporous silica nanoparticles (MSNs) and cross-linked poly(N-isopropylacrylamide) homopolymer and its copolymer with methacrylic acid was synthesized. The polymer was preferentially grafted on the outer surface of silane linker-functionalized MSNs based on free radical polymerization. The successful chemical grafting of the polymer on the silica surface was confrmed by FTIR, NMR, TG, and elemental analyses. The polymer contents of the hybrid particles vary from 18 to 40 % as determined by thermogravimetric and elemental analyses. The polymer content was tailored by varying diferent reaction parameters including monomer concentration, linker content/type, and reaction time. Well-defned uniform core-shell structured spherical particles with an average particle size of 367 ± 25 nm and shell thickness of 29 ± 8 nm were observed in TEM analysis. According to XRD and nitrogen physisorption studies, the ordered mesopore structure of the core MCM-48-type MSNs was maintained after an extended polymer grafting process and surface coverage with a high content of polymer. No signifcant pore blockage was observed in porosimetry analysis. More than 75% of specifc surface area, 68% of total pore volume, and the mean mesopore diameter were retained after successful grating of polymer on the outer silica surface. The pore volume thus can provide enough space to encapsulate high contents of cargo molecules for applications. The narrow pore width distribution of the main mesopores of silica determined by PALS analysis corresponds to the N2 sorption analysis and further confrms the uniformity of the mesopores
Data publication: Code for performing simulations on the evolutionary stability of territorial retention strategies.
No full textThis is the supplementary material for the submission of "Heterogenous and continuous resource distribution promote diversity in territorial behavior." to the journal "Ecological modelling". In this dataset, one can find the simulation code used to determine the evolutionary stability of 4 territorial strategies: cautious, common-sense, paradoxical, and daring. Strategies varied in their space utilization after losing or winning a conflict. Simulations.r contains the code for running the simulation and generating the data files presented in data/paper II. However, for the simulation to run, it needs acessory functions which are coded in Library/simulation library.r. Figures.r is the code used to generate the figures 1-7 in the paper. Analysis on number of conflicts.r contains figure 8 and the analysis that lead to it.This work was funded by CNPQ, the national council for technological and scientific development of Brazil, under grant number [152160/2018-3]. This work was funded by the Center of Advanced Systems Understanding (CASUS), which is financed by Germany's Federal Ministry of Education and Research (BMBF) and by the Saxon Ministry for Science, Culture and Tourism (SMWK) with tax funds on the basis of the budget approved by the Saxon State Parliament
Data publication: Geochemistry and fluid inclusion analyses of the Sadisdorf Li-Sn-(W-Cu) magmatic-hydrothermal greisen and vein system, eastern Erzgebirge, Germany
No full textThis data repository contains the sample locations and descriptions as well as the result for whole-rock, microthermometric and Raman analyses for the publication: “ The spatial and temporal evolution of the Sadisdorf Li-Sn-(W-Cu) magmatic-hydrothermal greisen and vein system, eastern Erzgebirge, Germany”
LDOS/SNAP data for MALA: Beryllium at high temperatures
No full text# Authors:
- Fiedler, Lenz (HZDR / CASUS)
- Cangi, Attila (HZDR / CASUS)
# Affiliations:
HZDR - Helmholtz-Zentrum Dresden-Rossendorf
CASUS - Center for Advanced Systems Understanding
# Dataset description
- System: Be256
- Temperature(s): 3750K, 7500K, 10000K
- Mass density(ies): 1.915 gcc
- Crystal Structure: bcc (material mp-20 in the materials project)
- Number of atomic snapshots: 50
- 30 (3750K)
- 10 (7500K)
- 10 (10000)
- Contents:
- ideal crystal structure: no
- MD trajectory: no
- Atomic positions: no
- DFT inputs: no
- DFT outputs (energies): yes
- SNAP vectors: no
- LDOS vectors: yes (partially, see below)
- dimensions: 160x80x80x250
- note: LDOS parameters are the same for all sizes of the unit cell
- trained networks: no
# Data generation
Ideal crystal structures were obtained using the Materials Project. (https://materialsproject.org/materials/mp-87/)
DFT-MD calculations were performed using the Vienna Ab initio Simulation Package (https://www.vasp.at/, VASP). DFT calculations were performed using QuantumESPRESSO.
For the VASP calculations, the standard VASP pseudopotentials were used. For Quantum Espresso, pslibrary was used (https://dalcorso.github.io/pslibrary/).
The LDOS was preprocessed using MALA.
# Dataset structure
Each temperature folder contains the following folders:
- ldos: holds the LDOS vectors (LDOS was not calculated for all snapshots!)
- dft_outputs: holds the outputs from the DFT calculations, i.e. energies in the form of a QE output file
Please note that the numbering of the snapshots is contiguous per temperature/mass density/number of atoms, and only data used in publications has been uploaded at this poin
dynamic contact angles of water of uncoated and coated (heptadecyl punicine) on quartz, hiddenite and kunzite
No full textdata sets of dynamic contact angle measurements of water onuncoated and coated (heptadecyl punicine) hiddenite, kunzite and quartz.
Measurements were carried out at the OCA25 from DataPhysics Instruments GmbH with the ARCA method.files are named as follows:
mineral_coated/uncoated_numer of experiment
minerals:
H1- hiddenite1
H2 - hiddenite 2
K1 - kunzite 1
K2 - kunzite 2
K3 - kunzite 3
Q1 - quartz 1
Q2 - quartz 2
Q3 - quartz 3
coating:
unb - uncoated
C17 - coated with a monolayer of heptadecyl punicin
Self-folding of two-dimensional thin templates into pyramidal micro-structures by a liquid drop - a numerical model
No full textSource code associated with publication entitled "Self-folding of two-dimensional thin templates into pyramidal micro-structures by a liquid drop - a numerical model"
src.tar.gz: c++ source code
scripts.tar.gz: figures
manuscript.tar.gz: text
ca70_side5_ec2.0.tar.gz: Simulation data obtained for Ca=70 deg, N = 5 and Ec = 2
ca90_side5_ec2.0.tar.gz: Simulation data obtained for Ca=90 deg, N = 5 and Ec =