Journal: Nature Communications

Article Title: Comprehensive catecholaminergic projectome analysis reveals single-neuron integration of zebrafish ascending and descending dopaminergic systems

doi: 10.1038/ncomms1171

Figure Lengend Snippet: ( a ) Scheme of dopaminergic (DA; blue) and noradrenergic (NA; red) cell groups and catecholaminergic (CA) tracts (grey) in 4 d.p.f. zebrafish larvae . Left: lateral view of forebrain and midbrain; right: dorsal view of CNS. Dark blue indicates dorsal-most and light blue ventral-most DA groups. Diencephalic DA groups: (DC1) ventral thalamus and periventricular posterior tuberculum; (DC2, DC4) large neurons in posterior tuberculum; (DC5, DC6) medium-sized neurons in posterior tuberculum and hypothalamus; (DC3) medial hypothalamus; (DC7) caudal hypothalamus; PO, preoptic region; POa, anterior preoptic region; Pr, dorsal pretectum; AC, retinal amacrine cells. Telencephalic DA groups: SP, subpallium; OB, olfactory bulb. NA groups: LC, locus coeruleus; MO, medulla oblongata interfascicular zone and vagal area and AP, area postrema. ac, anterior commissure; act, anterior CA tract; eht, endohypothalamic tract; mlct, medial longitudinal CA tract; pc, posterior commissure; poc, postoptic commissure; poht, preopticohypothalamic tract; prp, pretectal projections; prtep, pretectotectal projections. ( b–e ) In silico separation of individual neurons (arrowheads in b ) and their projections from whole-mount confocal image stack raw data. ( b ) Unprocessed maximum intensity projection (MIP) of a 4 d.p.f. larval brain. Blue masks D and L were manually drawn on the MIPs using ImageJ to separate soma and projections, based on visual discrimination. Bottom-most panel shows an example for computation of 3D segmentation mask M for a single neuron in the AP, based on the drawn masks D and L . The resulting 3D mask M was applied to the green channel to isolate the neuron and its projections. ( c ) Visualization of segmented AP neuron shown in ( b ) with projections. Quality control (QC; cyan) was carried out in 3D space within the region of interest (between dotted lines) to ensure the masks did not omit any GFP-labelled features belonging to the particular neuron. ( d , e ) Visualization of segmented individual soma and projections of GFP-labelled ( d ) amacrine cell (arrowheads) and ( e ) NA neuron in the MO interfasicular zone (IZ; arrowheads). See . Anterior at left, dorsal at top; anti-TH (red), anti-GFP (green); Dor, dorsal view; Lat, lateral view. Scale bars, 20 μm.

Article Snippet: The user proceeded to draw the dorsal and lateral segmentation masks over the MIPs using our ImageJ HDF5 plugin ( http://lmb.informatik.uni-freiburg.de/lmbsoft/imagej_plugins/ ).

Techniques: In Silico, Control

Journal: Frontiers in Neuroinformatics

Article Title: Reproducible supervised learning-assisted classification of spontaneous synaptic waveforms with Eventer

doi: 10.3389/fninf.2024.1427642

Figure Lengend Snippet: The supported file formats for data input, output and figures within Eventer.

Article Snippet: Neurodata without borders binary (HDF5) file v2 ( * .nwb) , , .

Techniques: Plasmid Preparation

Journal: F1000Research

Article Title: Best practice data life cycle approaches for the life sciences

doi: 10.12688/f1000research.12344.2

Figure Lengend Snippet: Overview of common standard data formats for ‘omics data. A more complete list can be found at FAIRsharing .

Article Snippet: Raw DNA/RNA sequence , FASTA FASTQ HDF5 SAM/BAM/ CRAM , FASTA is a common text format to store DNA/RNA/Protein sequence and FASTQ combines base quality information with the nucleotide sequence. HDF5 is a newer sequence read formats used by long read sequencers e.g. PacBio and Oxford Nanopore. Raw sequence can also be stored in unaligned SAM/BAM/ CRAM format , https://support.hdfgroup.org/HDF5/ https://samtools.github.io/hts-specs/ https://www.ncbi.nlm.nih.gov/ sra/docs/submitformats/ http://www.ebi.ac.uk/ena/ submit/data-formats .

Techniques: Sequencing, Functional Assay, Construct, Mass Spectrometry, Nuclear Magnetic Resonance

Journal: Materials

Article Title: Machine Vision for As-Built Modeling of Complex Draped Composite Structures

doi: 10.3390/ma14030682

Figure Lengend Snippet: HDF5 file structure with discrete data on material and geometry.

Article Snippet: By using the image analysis system and the ANSYS HDF5 import interface, a direct evaluation of the actual as-built properties of fiber composite components is made possible.

Techniques: