Lmst

#tomography

✨ Ever wondered how to effortlessly apply lazy expressions to massive tomographic HDF5 datasets and visualize them instantly in Cat2Cloud? 🤯

🎬 Check out this fantastic new video from our very own Luke Shaw! Discover how a bit of Python 🐍 magic and our user-friendly web interface simplify the process.

👇 Watch the full video to see the magic unfold: https://ironarray.io/cat2cloud

#HDF5 #Tomography #LazyEvaluation #DataVisualization #Cat2Cloud

is happy to have spent *so much* time on automated extraction of single fish from 20 combined tomographic scans (20 x 6 fish) a while ago. Because re-doing this on a fresh TB batch of 8 scans (48 fish) of nearly equal fish is done in half a morning. See https://github.com/habi/sticklebacks for the #Jupyter notebooks. #tomography #ecology

Screenshot of napari with loaded 3D data

Biomass - ESA's Forest Mission – Mapping Biomass From Space - Overview Video
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#GIS #spatial #mapping #biomass #satellite #remotesensing #earthobservation #spatialanalysis #spatiotemporal #vegetation #forest #radar #canopy #tomography #imaging #geomorphometry #forests #carbon #carbonaccounting #climatescience #management #planning #ecosystems #ESA

Biomass - ESA's Forest Mission – Mapping Biomass From Space
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https://www.esa.int/Applications/Observing_the_Earth/FutureEO/Biomass <-- shared Biomass information hub
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#GIS #spatial #mapping #biomass #satellite #remotesensing #earthobservation #spatialanalysis #spatiotemporal #vegetation #forest #radar #canopy #tomography #imaging #geomorphometry #forests #carbon #carbonaccounting #climatescience #management #planning #ecosystems
#ESA

is happy to hear that https://doi.org/10.1101/2024.11.10.622888 “has been judged scientifically suitable for publication" in PLOS One after a round of peer review. Once "it meets all outstanding technical requirements" it will be published online. For the moment you all have to read the bioRxiv version. And can nonetheless already look into the full dataset yourself, for example at https://webknossos.org/links/U8wuIdhmfzWMr7rm

#tomography #microct #femaleanatomy #science

Biopsie-Stanze direkt aus dem Operationssaal ins 3D-#Röntgenmikroskop.

Das ist heute 1 spannendes FirstTime für die #GINIX @ @DESY #Synchrotron.

#XRayImaging #Tomography

A $100 DIY muon tomographer
https://spectrum.ieee.org/diy-muon-tomography
#ycombinator #arduino #geiger_counter #muons #remote_sensing #tomography #type_departments

$100 Muon Detector Lets You Harness the Cosmos
https://spectrum.ieee.org/diy-muon-tomography
#ycombinator #arduino #geiger_counter #muons #remote_sensing #tomography #type_departments

In unserer onlinenen #Ringvorlesung heute:

Basics of #XRay #Imaging and Computed #Tomography #CT

15:30 Uhr mit @mosterh1 von der @unigoettingen

Einwahl: https://kit-lecture.zoom-x.de/j/65527468773?pwd=axMdaXp5Jebvan8TVz9qbo4bkL3MHl.1

Kenncode: whsj=71J

#Synchrotron #Röntgen #Forschung #NFDIRocks

Vortragsfolie, Titel: „The Many Dimensions of X-Ray Imaging II“.

Gezeigt wird in vielen symbolischen Koordinatensystemen ein Überblick über verschiedene Parameter (Beispiele: Belichtungszeit, Wellenlänge, Dimensionalität, Gesichtsfeld; aber auch Konzepte wie Fern- und Nahfeld, Vollfeld und Raster; Rekonstruktionsverfahren ohne, Einzelschritt, iterativ) bei der Bildgebung vermöge Röntgenstrahlung; in rot überlagert sich weitere Stichworte (etwa: Holografie, Ptychografie, Gerchberg-Saxton-Algorithmus; pink beam vs Si-111-Monochromator), welche spezielle Messmethoden charakterisieren.

New paper, just published in Physical Review X Energy, on the muography of the G3 nuclear reactor

by Baptiste Lefevre and co-authors
https://doi.org/10.1103/PRXEnergy.4.013002

The visualization software I developed for #Cosmology contributed in the mapping of the inner, inaccessible structure of the reactor.

▶️ see the video and interactive visualization here: https://journals.aps.org/prxenergy/abstract/10.1103/PRXEnergy.4.013002#supplemental

#Physics #Muography #Nuclear #NuclearReactor #science #STEM #engineering #Energy #G3 #Muons #MuonTomography #tomography

A screenshot captured on the frontpage of the Physical Review X Energy webpage showing an article thumbnail image, title, summary and other details. Title reads "3D Reconstruction of a Nuclear Reactor by Muon Tomography: Structure Validation and Anomaly Detection". Summary reads "Muon tomography, a non-invasive technique that can be used to image large, inaccessible structures, is combined with machine learning to create a 3D reconstruction of a historical nuclear reactor that reveals material density variations, including potential anomalies in the graphite core." Dated 28 January, 2025. Thumbnail image shows a 3D reconstructions and slices of the density field of the reactor.

A screenshot of a figure of the article, featuring a black on white technical drawing mixed with a colorful 3D visualization. Captions reads "3D visualization of the postprocessing of SART’s real data reconstruction, showing an isosurface of the density field 𝑑 =1.5 together with a 𝑦 =0 slice and the corresponding technical drawing. This 3D visualization is complemented by a video in Supplemental Material".

A screenshot of a figure of the article, featuring a colorful 3D visualization against a white background. Caption reads "3D visualization of the postprocessing of SART’s real data reconstruction, showing an isosurface of 𝑑 =1.5 together with 𝑦 =0 and 𝑧 =0 slices. This three-dimensional rendering of the density field is complemented by an interactive 3D visualization in Supplemental Material".

Gleich beginnt die nächste Postersitzung beim #DESY Nutzerinnentreffen #UM25 – mein heutiger Beitrag:

"#FPGA Based Live-Reco for #Tomography: Preparing for 4th Generation Data Rates"

Mit dem Upgrade zum #PetraIV #Synchrotron erwarten wir eine rund hundertfach höhere Datenrate, speziell in der Parallelstrahl-#Tomografie an der #GINIX könnten es ca. 3 Petabyte täglich werden. Hier studieren wir eine Live-Rekonstruktion des Datenstroms mittels programmiererbarer Hardware.

https://sci.photos/QR/UM25/#ginix

Das wissenschaftliche Poster beschreibt den Einsatz von FPGAs (Field Programmable Gate Arrays) in der Echtzeit-Tomographie und deren Vorbereitung auf die Datenvolumen der vierten Generation von Synchrotronstrahlungsquellen. Es wurde von der Universität Göttingen und DESY Photon Science entwickelt.

– FPGA Based Live-Reco for Tomography: Das Poster stellt dar, wie FPGAs verwendet werden, um die Datenverarbeitung in der Tomographie zu optimieren, insbesondere für das Göttingen Instrument for Nano-Imaging with X-Rays (GINIX) an den PETRA III und IV Strahlrohren.
– Contrast Transfer Function - Fourier Filter: Es wird erläutert, wie die Kontrastübertragungsfunktion mit Hilfe eines Fourier-Filters modelliert und als Faltung im Realraum implementiert wird. Hierbei werden Vorteile der FPGA-basierten Verarbeitung, wie schnelle Fourier-Transformationen und Realraumfaltungen, diskutiert.
– Fourier vs. Convolution: Vergleich der Methoden in Bezug auf die Bildrekonstruktion und Datenverarbeitungseffizienz.
– GINIX II @ PETRA IV: Processing Problem: Ein Abschnitt des Posters befasst sich mit den Herausforderungen der Datenverarbeitung bei hochauflösender Nano-Bildgebung, wobei Lösungsansätze über FPGAs aufgezeigt werden.
– FPGAs as Pipelined Streaming Processor: Hier wird die Überlegenheit von FPGAs gegenüber traditionellen CPUs hervorgehoben, insbesondere hinsichtlich ihrer Programmierbarkeit und Fähigkeit zur Verarbeitung von Streaming-Daten.

[ChatGPT 4o]

Atop The Oregon Cascades, [Research] Team Finds A Huge Buried Aquifer
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https://www.eurekalert.org/news-releases/1069774 <-- shared technical article
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https://doi.org/10.1073/pnas.2415155122 <-- shared paper
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https://www.usgs.gov/centers/oregon-water-science-center/science/mckenzie-river-source-water-study <-- shared USGS technical article, 2011, ‘McKenzie River Source Water Study’
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https://youtu.be/6R8e5HwGMwU?si=sniW4bvvzzviTYie <-- shared media video overview
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#GIS #spatial #mapping #model #modeling #water #hydrology #Oregon #Cascades #CascadeMountains #PNW #PacificNorthwest #volcanic #rocks #aquifer #waterresources #watermanagement #climatechange #snowpack #drought #spatialanalysis #CriticalZone #geohazards #geology #engineeringgeology #landscapes #weathering #bedrock #holocene #groundwater #structuralgeology #orogeny #remotesensing #geophysics #sampling #drilling #porosity #permability #tomography #lava #spring #seep #breccia #discharge #streams #runoff #precipitation #climate #rainfall #recharge

photo - Scientists examine a large-volume spring in young volcanic rocks of the McKenzie River watershed on the west side of the Cascade topographic crest that was monitored as part of this study. Credit: Benjamin Nash

map, photo and charts - (A) Electrical resistivity tomography of Olallie North Spring, which emerges along a flow contact of _25 ka Scott Mountain lava flows. Lateral variations correspond to spring discharge points along the lava flow basal breccia such as depicted in (B) (photo: Benjamin Nash). (C) Mean of total yearly range in discharge _Q divided by mean annual flow Qavg versus average upstream age for springs and streams. The horizontal line defines “spring-” versus “runoff-” dominated. (D) SD of yearly average summer discharge (June–September), normalized by Qavg, with CZ state shift labeled.

$maps and chart - (A) Distribution of geothermal drill holes. Thin black circles’ radii scale with total logged length, and colors indicate the fraction of length for which dT=dz < 20_C/km (implying downward flux of meteoric water). Red circles are the fraction with inverted gradients (dT=dz < 0_C/km). The purple contour indicates bedrock ages <2 Ma, while stars mark Holocene age phreatomagmatic eruption vents. (B) Two example temperature-depth logs from deep wells in old and young bedrock. (C) Porosity (blue) and resistivity (orange) in the Santiam Pass drill hole SP 77-24. Dashed lines indicate low porosity at high measured resistivity. (D) Chemical weathering tracked by oxidation state of iron in the Santiam Pass drill hole. The green box indicates range of Quaternary High Cascades lavas (SI Appendix), indicating that much of the SP 77-24 hole has been oxidized.$

maps and cross section - Oregon Cascades study site. (A) Topography, rivers (from USGS blue lines), stream gauges, lakes, and faults. Olallie North Spring (ONS) and HJ Andrews Experimental Forest (HJA) are labeled. (B) Surface bedrock ages (18), geothermal drill holes, and Quaternary volcanic vents (19). Labeled vents exhibited Holocene phreatomagmatic activity: Sand Mountain volcanic field (SMF), Blue Lake Crater (BLC), Twin Craters (TC). Gray areas are mapped as “Sedimentary deposits and rocks” in ref. 18. (C) Cross-section of swath topography and surface bedrock ages (N-S average of _4 km from Santiam Pass, pink box in panel A), with subsurface structures based on published geologic maps (SI Appendix). The proposed Critical Zone (CZ) state shift and physiographic “Western” and “High” Cascade provinces are labeled. (D) Temperature gradient versus depth in drill holes from panel (C). Near-isothermal or inverted temperature gradients define the “rain curtain.”

These Revolutionary Maps Are Revealing Earth’s Geological Secrets
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https://www.zmescience.com/science/tectonic-model-beatiful-new/ <-- shared technical article
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https://doi.org/10.1016/j.earscirev.2022.104069 <-- shared paper
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#GIS #spatial #mapping #tomography #geology #remotesensing #structuralgeology #plates #platetectonics #earth #global #model #modeling #opendata #opensource #spatialdata #vector #platemodel #mechanics #GPS #earthquakes #volcanoes #topography #orogeny #tectonics #spatiotemporal #spatialanalysis #Pangea #Gondwana #Gondwanaland #ReuniteGondwanaland #Laurasia #lithosphere #crust #mantle #core #geophysics #geochemistry #geochronology #dating #Mesoproterozoic

map - tectonic plates and geologic processes

map - Models of the Capricorn Plate and associated Mid-Indian deformation zone.

map - Magnetic anomaly map of southern Africa overlaying topographic relief. The WDMAM_V2 magnetic model has a pixel size of 1.5 minutes, which is approximately 2.8 km at the equator. The model is created from shiptrack, airborne and satellite datasets resulting in variable resolution that is evident in this image and affects the accuracy of province boundaries.

maps - map of the last orogenic event to affect a province. The colors are approximately related to the age of the orogenic event. The points show locations of observed and estimated metamorphic ages

#OPTImAL: #Optical projection #tomography implemented for #OpenSource accessibility & low cost:

-#LED excitation
-#motorized rotation stage
-#GPU-based #image reconstruction (#MATLAB/#ASTRA)

https://doi.org/10.1098/rsta.2023.0101
#DIYbio #lab #instruments #fluorescence #imaging #MicroManager

Geologists Stunned On Discovering A Part Of The Earth That Disappeared 20 Million Years Ago
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https://www.good.is/geologists-stunned-at-discovery-of-earths-ancient-mega-plate-they-didnt-know-about-at-all-ex1 <-- shared technical article
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https://doi.org/10.1016/j.gr.2023.09.013 <-- shared paper
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https://youtu.be/VyEUWySaFPc?si=rzUiIh14GxmiC0l- <-- reconstruction animation
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#GIS #spatial #mapping #remotesensing #geomagnetism #argoland #kinematicreconstruction #platetectonics #GPlates #junctionregion #PhilippineSeaPlate #Borneo #NewZealand #Japan #Zealandia #Philippines #NewGuinea #junction #subduction #plates #geology #structuralgeology #pontus #pontusplate #paeleogeography #geologichistory #Zealandia #seismology #spatialanalysis #spatiotemporal #tomography #model #modeling

maps - the Pangea-Tethys and Panthalassa plate tectonic realms separated by the Juction Region

map - tectonics of the Philippine Sea Plate, highlighting the different microplates that formed as a result of oceanic spreading at different spreading centers

Researchers explore a #single_cell using advanced #X_ray imaging techniques.

#tomography #fluorescence #microscopy

https://phys.org/news/2024-07-explore-cell-advanced-ray-imaging.html

ABI EIT: A wearable #OpenSource electrical #impedance #tomography (#EIT) device:

-#medical #imaging
-monitoring #lung/#cardiac function, #brain activity
-cost: ~US$260
-#3Dprinted parts
-#Teensy controller

https://doi.org/10.1016/j.ohx.2024.e00521
#DIYbio #lab #instruments #medicine #diagnostics

Keynote by Joost Batenburg: Real-time #Imaging Pipelines for #Tomography

- filtered back projection: einfacher & schneller Algorithmus, Messung nicht ideal genug
- iterative Rekonstruktionen: langsam
- algebraische Filter: schnell & gut

#HIConference2024 #HelmholtzImaging