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ShareScore release 0.9.0
Dataset results
7 results for “ImageJ”
Como calcular a quantidade de proteína/DNA em uma banda com o ImageJ
<p>Esse vídeo é sobre como realizar análise de densitometria utilizando o ImageJ.</p> <p>Link no youtube: https://www.youtube.com/watch?v=NJO0CLwwpmw</p> <p> </p> <p><strong>Info:</strong></p> <p>Lingua: Português</p> <p>Programa: FIJI - Fiji is just ImageJ</p> <p>Imagem gel utilizada:</p> <ul> <li> File: SDS-PAGE with Taq DNA Polymerase.JPG</li> <li>Author: Marta Ferreira (MPCF)</li> <li>Multi-licensed under the GFDL and all CC-By-SA</li> <li>Link: https://commons.wikimedia.org/wiki/File:SDS-PAGE_with_Taq_DNA_Polymerase.JPG</li> </ul> <p>Imagem gel artificial</p> <ul> <li>File: Fake_gel.png</li> <li>Author: Molino, JVD</li> <li>Made in: Inkscape</li> </ul>
ImageJ-processed Images from the BBBC022 dataset
<p>Processed microscopy images from the Cell Painting dataset BBBC022. 5 fluorescence channel images converted to RGB images with ImageJ and resized to 224x224 pixels. The CSV files contain the metadata (b22_dataset.csv all data points, b22_dataset_mesh_nonans.csv only MeSH annotated data points).</p>
Dataset of confocal microscopy stacks from plant samples - ImageJ SurfCut: a user-friendly, high-throughput pipeline for extracting cell contours from 3D confocal stacks
<p>This data set contains confocal stacks from <em>Arabidopsis thaliana </em><em>35S::GFP-MBD</em> light grown hypocotyl as well as propidium iodide stained cotyledon pavement cells and shoot apical meristem. This is the test dataset for the Fiji macro SurfCut (https://github.com/sverger/SurfCut; 10.5281/zenodo.2635737)</p> <p> </p> <p><strong>Material and methods:</strong></p> <p>Plant material and growth conditions</p> <p><em>Arabidopsis thaliana </em>wild type Col-0 and the microtubule reporter line <em>GFP-MBD</em> (WS-4, (Marc et al. 1998) were used. Seeds were cold treated for 48 hr to synchronize germination. Plants were then grown in a phytotron at 20°C, in a 16 hr light/8 hr dark cycle on solid Murashige and Skoog medium (MS medium, Duchefa, Haarlem, the Netherlands) with 0.8% agar, 1% sucrose, and no vitamin.</p> <p> </p> <p>Confocal microscopy</p> <p>Cell contour staining in the case of PC_PI_Col0_(1-8).tif and SAM_PI_Col-0.tif was performed by staining the cell wall with Propidium Iodide (PI). Plants were immersed in 0.2 mg/ml propidium iodide (PI, Sigma-Aldrich) for 10 min and washed with water prior to imaging. For imaging, samples were either placed on a solid agar medium and immersed in water, or placed between glass slide and coverslip separated by 400 μm spacers to prevent tissue crushing. Images were acquired using a Leica TCS SP8 confocal microscope, equipped with a water immersion objective (HCX IRAPO L 25x/0.95 W). PI excitation was performed using a 552 nm solid-state laser and fluorescence was detected at 600–650 nm. GFP excitation was performed using a 488 nm solid-state laser and fluorescence was detected at 495–535 nm. Stacks of 1024x1024 pixels (pixel size of 0.363 x 0.363 micron) optical section were generated with a Z interval of 0.5 μm.</p> <p> </p> <p><strong>File list:</strong></p> <p>Light grown hypocotyl, <em>GFP-MBD</em> reporter line:</p> <p>- Hypocotyl_GFP-MBD.tif</p> <p>Cotyledon’s pavement cells, PI staining:</p> <p>- PC_PI_Col0_1.tif</p> <p>- PC_PI_Col0_2.tif</p> <p>- PC_PI_Col0_3.tif</p> <p>- PC_PI_Col0_4.tif</p> <p>- PC_PI_Col0_5.tif</p> <p>- PC_PI_Col0_6.tif</p> <p>- PC_PI_Col0_7.tif</p> <p>- PC_PI_Col0_8.tif</p> <p>Shoot apical meristem, PI staining:</p> <p>- SAM_PI_Col-0.tif</p> <p> </p> <p><strong>Reference:</strong></p> <p>Marc, Jan, Cheryl L. Granger, Jennifer Brincat, Deborah D. Fisher, Teh-hui Kao, Andrew G. McCubbin, and Richard J. Cyr. 1998. “A GFP–MAP4 Reporter Gene for Visualizing Cortical Microtubule Rearrangements in Living Epidermal Cells.” <em>The Plant Cell</em> 10 (11): 1927–39. https://doi.org/10.1105/tpc.10.11.1927.</p>
A sample image data for ImageJ Bleach Correction Plugin
<p>This sample image data is for testing the ImageJ Bleach Correction plugin. Data was acquired by Boryana Petrova in the Christian H. Haering Lab (EMBL) in 2011 and provided as a sample for development to Kota Miura</p> <p><a href="https://imagej.net/Bleach_Correction">https://imagej.net/Bleach_Correction</a></p> <p>For more details, see "README.md".</p>
ImageJ ROI bug
<p>ROI sets jump around on image when reopened</p>
20230315 ImageJ bio-format importer multi-channel ND2 bug
<p>A bug wherein ND2 images taken with different camera settings are read incorrectly by ImageJ's bio-format importer</p> <p>imageJ_test.nd2 - The ND2 file produced by NIS Elements AR on a Nikon LV100 microscope. 11 time steps, 2 channels (images taken with different filter blocks).</p> <p>test_image_ImageJ.jpg - A screenshot of Fiji/ImageJ after opening the ND2 with bio-formats importer. The number of dimensions is correct (11 time steps, two channels) but each channel is mono rather than an rgb image and the images are badly jumbled.</p> <p>test_image_metadata_ImageJ.jpg - The OME metadata of the ND2.</p> <p>test_image_movie_imageJ.avi - The ImageJ output exported as an AVI.</p> <p>test_image_NIS.jpg - A screenshot of the ND2 opened in Nikon's NIS Elements Viewer.</p> <p> </p> <p> </p> <p> </p>
ImageJ OIB test files
<p>.oib and .oif test files that do not open in ImageJ likely due to Bioformats bug</p>
ScienceDex guides
Understand access before you commit
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.