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8 results for “bioimage analysis”
Dynamic FRET example videos related to "Mars, a molecule archive suite for reproducible analysis and reporting of single-molecule properties from bioimages"
<p>Videos of dynamic switching between iso-I and iso-II conformations of a holiday junction at 50 mM Magnesium resulting in high and low FRET from Cy3 and Alexa647 labels positioned on the arms. Holiday junctions are surface immobilized through a biotin attachment and imaged using TIRF microscopy. The camera sensor is split using a dual view so that the acceptor emission is on the top and the donor emission is on the bottom. Videos from each position are provided as compressed zip files containing a sequence of tif files and associated metadata text file. Image sequences were collected using Micro-Manager 2.0 using ALEX or alternating laser excitation with alternating 637 and 532 pulses separated as two different channels. Beam profile images are provided for 637 and 532 excitation allowing for correction of the non-uniform beam profiles. The following 2D affine transformation matrix can be used to transform from the top acceptor emission region to the bottom donor emission region during processing.</p> <p>Affine 2D transformation from top to bottom: (m00, m01, m02, m10, m11, m12), (1.00276, 0.000208, 1.01236, 0.000267, 1.00312, 507.21025)</p> <p>A detailed image processing workflow for this dataset using Mars can be found under the example section at <a href="https://duderstadt-lab.github.io/mars-docs/">https://duderstadt-lab.github.io/mars-docs/</a> or directly at <a href="https://duderstadt-lab.github.io/mars-docs/examples/FRET_dynamic/">https://duderstadt-lab.github.io/mars-docs/examples/FRET_dynamic/</a></p>
Research data management for bioimaging: the 2021 NFDI4BIOIMAGE community survey - Extended Data 4 - Analysis Data Sheet
<p>This dataset is extended data to the manuscript "Research data management for bioimaging: the 2021 NFDI4BIOIMAGE community survey" by Schmidt C., Hanne J, Moore J, Meesters C, Ferrando-May E, Weidtkamp-Peters S, and members of the NFDI4BIOIMAGE initiative. [version 1; peer review: awaiting peer review] F1000Research 2022, 11:638, https://doi.org/10.12688/f1000research.121714.1</p> <p>This extended data includes:</p> <p>- Data Analysis Sheet and results table</p> <p>Note: The data is anonymized (i.e., all IP addresses as well as personal comments were deleted)</p> <p>The revised version was published after the peer-review process of the original article on zenodo.org</p>
Section 5.4 "Task Area 4: Bioimage informatics and analysis" Figure 11
<p>Figure 11. <em><span>FAIR pipelines for image analysis to balance the current status quo of hardly recordable manual processing (point-and-click) with the goal of increasing reproducibility of workflows</span></em>.</p> <p>from NFDI Grant Application, "<strong>National Research Data Infrastructure for Microscopy and Bioimage Analysis</strong>" (NFDI4BIOIMAGE)</p>
Introduction to Bioimage Analysis using QuPath (supporting image)
<p>Example image supporting the workshop "Introduction to Bioimage Analysis using QuPath", in-person at HMS.</p>
Data sets for "Automated cell segmentation for reproducibility in bioimage analysis"
<p>This is the raw data sets used in "Automated cell segmentation for reproducibility in bioimage analysis", published in Synthetic Biology (Oxford Academic)</p>
Dataset for interactive course on BioImage Analysis with Python (BIAPy)
<p>This dataset can be used to run the course on image processing with Python available here: <a href="https://github.com/guiwitz/neubias_academy_biapy">https://github.com/guiwitz/neubias_academy_biapy</a></p> <p>It combines microscopy images from different publicly available sources. All files are either in the Public Domain (PD) or released with a CC-BY license. The list of the original location of the data as well as their licenses can be found in the LICENSE file.</p>
The Twenty Questions of Bioimage Object Analysis
<p>A proposed 20 question schema for creating object analyses in bioimages. </p>
Bioimage Analysis Introduction Practical
<p>An introduction to image analysis and napari for Master level education</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.