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The DLA-RMR dataset: Annotated subset of RMR notebooks for CVC development
No full textWhat’s new in this version: The dataset now contains 100 fully annotated images instead of only 50.
This dataset is structured into four components, each serving a distinct role in the development of a document analysis system.
Word-level annotations are provided in the file word_annotations_for_cropped_images.json. These annotations describe the images contained in the cropped_images folder. Each entry specifies the location of a word as a polygon, together with its orientation (horizontal, vertical, or tilted) and the type of writing implement used (ink or pencil). Additional metadata, such as bounding boxes and segmentation areas, is also included.
Cropped images are stored in the cropped_images folder. This set comprises 50 images, each containing only the primary page extracted from the corresponding full notebook scans.
Full images are located in the full_images folder. This collection also contains 50 items, representing the complete notebook scans in which the primary page appears alongside other material.
Page-level annotations are contained in the page_annotations folder. These are provided in YOLO format, with a single class (page) defined in classes.txt. Each annotation file specifies the bounding box of the primary page within the corresponding image in the full_images folder.
Examples illustrate the annotation structure. In the JSON file, a typical word annotation records polygon coordinates, the attribute "orientation": "horizontal", and "writing_tool": "pencil". In the YOLO annotations, a sample entry such as 0 0.499023 0.500776 0.777344 0.816912 denotes the normalised coordinates of the primary page bounding box.
Acknowledgement:
The research for this work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy - EXC 2176 ‘Understanding Written Artefacts: Material, Interaction and Transmission in Manuscript Cultures’, project no. 390893796. The research was conducted within the scope of the Centre for the Study of Manuscript Cultures (CSMC) at Universität Hamburg.
The images are taken from notebook pages of Rainer Maria Rilke, from the Deutsche Literaturarchiv Marbach (DLA), A:Rilke-Archiv Gernsbach.
We thank Hui Xu for her support in annotating the images
Data Set: Non-Equilibrium Anti-Stokes Raman Spectroscopy for Investigating Higgs Modes in Superconductors
No full textThis dataset contains the original data as published in Glier, Tomke E., et al. "Non-Equilibrium Anti-Stokes Raman Spectroscopy for Investigating Higgs Modes in Superconductors." (Nat Commun 16, 7027 (2025). https://doi.org/10.1038/s41467-025-62245-4). The dataset contains Non-Equilibrium anti-Stokes Raman Scattering (NEARS) spectra of Bi-2212. Stokes and anti-Stokes Raman data were recorded for A1g and B1g probe symmetry are are uploaded in seperate files. Raman shift in meV is given in the left column in each file. Detailed experimental information can be found in the attachment (data_summary.pdf) and the article
Simulation and reconstruction of the final momenta generated in the Coulomb explosion of iodopyridine
No full textThis entry contains data about the Coulomb explosion of 2-iodopyridine.
The simulation data contain the results of the simulation of the Coulomb explosion using the XMDYN software, under several conditions. The results contains the final momenta and charges of the ions produced in the explosion.
The reconstruction data contain the results of an algorithm that fits a Gaussian model to the final momenta of the ions in experimental condition (random molecule rotation, finite detection efficiency, unknown ion identity). The reconstruction has been applied to simulated data under several different condition and to experimental data collected at EuXFEL, at the SQS endstation.
The README.md file describe in more details the format of the other files.
The data in this entry has been used for the manuscript: "Imaging collective quantum fluctuations of the structure of a complex molecule" (in revision), and are shown in the following figures:
- Figure 2: `simulation_main.h5`, `simulation_no_GSF.h5`
- Figure 3: `reconstruction_simulation_C6_M3.h5`, `reconstruction_experimental_C6_M3.h5`
- Figure 4: `reconstruction_simulation_C6_M3.h5`, `hessian.dat`
- Figure S7: `simulation_main.h5`, `smulation_thermal_250K.h5`
- Figure S10: `simulation_main.h5`, `reconstruction_simulation_C6_M3.h5`
- Figure S11: all file `reconstruction_simulation_benchmark[..].h5`
- Figure S12: `reconstruction_simulation_C6_M3.h5`, `reconstruction_simulation_benchmark_C6_M3.h5`
- Figure S13: `reconstruction_simulation_C6_M3.h5`, `hessian.dat`
- Figure S14: `reconstruction_simulation_low_charges_C6_M3.h5`, `reconstruction_experimental_low_charges_C6_M3.h5`
- Figure S15: `reconstruction_experimental_C6_M3.h5
Simulation Code to Group Deliberation in Epsitemic Source Networks
No full textPython code for Monte Carlo Simulations to compute outcomes of simple group deliberations in random source networks with varying parameters
Pathology-oriented multiplexing enables integrative disease mapping
No full textProtein expression and location within tissues represent key determinants of health and disease. While advances in multiplexed imaging have expanded the number of proteins that can be spatially assessed, its potential use to integrate different biological layers (i.e., cell structure, subcellular domains and signal activity) remains unclear. Available methods are mainly restricted by the composition of antibody panels and image resolution, limiting the applications and development of computational image analysis tools. Here, we present Pathology-oriented multiPlexing (PathoPlex), a scalable, quality-controlled, and interpretable framework that combines deep multiplexed imaging at subcellular resolution with an open-source software package to extract, interpret and model protein co-expression patterns (clusters) that represent the integration of multiple biological layers. PathoPlex provides simple 3D printing solutions to simultaneously process up to 40 archival formalin-fixed paraffin-embedded biopsies (approx. 4000 mm2) using conventional inverted fluorescent light microscopes. We validated PathoPlex in 95 iterative cycles, mapping at least 142 commercial antibodies at 80 nm per pixel, which generated over half a trillion pixels. As proof-of-concept, we identified epithelial c-Jun activity as a key switch in immune-mediated kidney disease, demonstrating that PathoPlex-derived clusters represent functional pathological features. Next, PathoPlex was used to dissect human diabetic kidney disease (DKD), defining clusters associated with organ function, patient stratification, and therapeutic potential (i.e., calcium-mediated stress in proximal tubuli). Then, PathoPlex revealed clusters linked to renal stress in patients with type 2 diabetes (T2D) without DKD, providing tissue-based readouts to assess response to short-term administration of sodium-glucose cotransporter-2 inhibitors (SGLT2i). Finally, we proposed a cluster-based model connecting early T2D with DKD in patients without SGLT2i and evaluated the potential of SGLT2i to modify DKD development and progression. In summary, PathoPlex paves the way to democratize access to multiplexed imaging and support the development and interpretation of next-generation pathology atlases
Anleitung zu ReCKS: Eine Webapplikation für die linguistische Erforschung von Reddit-Kommentaren
No full textReCKS („Reddit Corpus Keyword Search“) ist eine Webapplikation zur Stichwortsuche in Reddit-Kommentaren aus dem größten deutschsprachigen Subreddit (r/de, derzeit über zwei Millionen registrierte Nutzer:innen). Das zugrunde liegende Korpus von ReCKS umfasst ca. 1 Million Kommentare aus dem Zeitraum 2006–2023. Zwei Suchstrategien stehen zur Verfügung: eine einfache feste Suche sowie eine erweiterte Suche mit regulären Ausdrücken (RegEx). Die Treffer werden in Tabellen- und Diagrammform dargestellt und können exportiert werden.
Diese Anleitung zu ReCKS v1.03 erläutert die verschiedenen Möglichkeiten der Abfrage im Detail. Sie bietet insbesondere eine Einführung in die Syntax regulärer Ausdrücke
The PHOENIX/1D NewEra model atmosphere grid: Access software & low resolution synthetic spectra
No full textTne NewEra paper has been published in A+A (https://ui.adsabs.harvard.edu/abs/2025A&A...698A..47H and 10.1051/0004-6361/202554171).
Software to access NewEra spectrum files (DOI 10.25592/uhhfdm.16727) from python and an example reader.
get_NewEra_from_FDR.py get a single model from the data repository.
example_read_HSR_H5.py reads data from a single model h5 file.
example_read_structure_from_HSR_H5.py reads and parses model structure data (radii, temperatures etc.)
example_read_gaia_fmt.py read the first spectrum of one of the GAIA format archives
list_of_available_additional_NewEra_models.txt: Additional NewEra HSR (V3) spectra and models added after the paper was published.
list_of_available_NewEraV3_models.txt: Version 3.0 of the NewEra spectra (much improve level dissolution for Teff>=5000K). Use these files!
list_of_available_NewEraV2_models.txt: Version 2.0 of the NewEra HSR spectra
list_of_available_NewEra_models.txt is a list of all available models, MD checksums, file sizes and download links.
Readme.PHOENIX.gaia_fmt.txt explains the format of the GAIA archive files
PHOENIX-NewEraV3-GAIA-DR4_v3.4-PHOTOMETRY.tar.gz archive with Version 3 of the GAIA DR4 photometry
PHOENIX-NewEraV3-GAIA-DR4_v3.4-SPECTRA.tar.gz archive with Version 3 of the GAIA DR4 spectra
PHOENIX-NewEraV3-LowRes-SPECTRA.tar.gz archive with Version 3 of all low resolution spectra
PHOENIX-NewEraV3-JWST-SPECTRA.tar.gz archive with Version 3 of all spectra in the JWST spectral range and resolution
PHOENIX-NewEraV2-GAIA-DR4_v3.4-PHOTOMETRY.tar.gz archive with Version 2 of the GAIA DR4 photometry
PHOENIX-NewEraV2-GAIA-DR4_v3.4-SPECTRA.tar.gz archive with Version 2 of the GAIA DR4 spectra
PHOENIX-NewEraV2-LowRes-SPECTRA.tar.gz archive with Version 2 of all low resolution spectra
PHOENIX-NewEraV2-JWST-SPECTRA.tar.gz archive with Version 2 of all spectra in the JWST spectral range and resolution
PHOENIX-NewEra-LowRes-SPECTRA.tar.gz archive with all low resolution spectra
PHOENIX-NewEra-JWST-SPECTRA.tar.gz archive with all spectra in the JWST spectral range and resolution
NewEra_for_GAIA_DR4.tar Synthetic spectra, colors and BCs in GAIA DR4 format as tar file, includes Readme
How to Erase Writing According to Recipes from the Arab World: Replication and Analytical Report - dataset: analyses of erased samples
No full textMulti analytical dataset of erased mockup samples, supporting the publication: "How to Erase Writing According to Recipes from the Arab World: Replication and Analytical Report".
The results are published in: Colini C., Marotta G., Sathiyamani S., Yañez Langner V., Muller A., Grigoriadou K., Yu C., How to Erase Writing According to Recipes from the Arab World: Replication and Analytical Report, in Cammarosano, M. (ed.) Erasing and Rewriting in Manuscript Cultures: Practices of Text Obliteration and Manuscript Reuse in a Global Perspective, Studies in Manuscript cultures, 48, De Gruyter, 2025
The samples were first examined and imaged using a three-colour Dino-Lite USB digital microscope (model AD413T-I2V), in combination with an external white-light source, to document any visible change in the sample after applying the erasing methods.
μ-XRF measurements: Spatial maps of a selection of samples were acquired using a Bruker M6 Jetstream scanner with a
Rh X-ray tube, a 60 mm2 Xflash SDD detector, and an adjustable measuring spot ranging from 100 to 1000 μm. The measurements were conducted at 35 kV voltage and 800 μA current, with a spot size of 35 μm, an acquisition time of 100 ms per spot, and a step size of 100 μm. The data was subjected to further analysis on the instrument’s software.
Fourier transform infrared spectroscopy (FTIR) spectra were acquired using a Nicolet iS5 FTIR spectrometer in combination with the iD7 ATR (attenuated total reflectance) module, equipped with a diamond crystal. The spectra were acquired in the range 4000–400 cm-1 with a total of sixty-four scans per measurement and a spectral resolution of 4 cm-1. The measurements were performed on both the
erased and non-erased areas of a selection of samples, in order to determine the
presence of residues, including organic components not detectable using μ-XRF spectroscopy. In specific cases, the reference spectrum of the ingredients was taken to facilitate comparison.
The data labelling follows the CSMC Artefact Profiling Lab Standardised System for the Labelling of Analytical Data (https://doi.org/10.25592/uhhfdm.14853
TEST- Erster Zwischenbericht zur Evaluation des Konsumcannabisgesetzes (EKOCAN)
No full textTESTUPLOAD: Erster Zwischenbericht zur Evaluation des Konsumcannabisgesetzes. Der Bericht gibt erste Einblicke in die bisherigen Entwicklungen seit Inkrafttreten des Gesetzes
The 'Vienna Agathangelos': Negotiating Philology and Damaged Cultural Heritage
No full text“The ‘Vienna Agathangelos’: Negotiating Philology and Damaged Cultural Heritage”, Manuscript Cultures in the Caucasus, CSCM, University of Hamburg