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Deformable 2D and 3D big data image registration and transformation with BigWarp

I2K 2024 From Images to Knowledge
Milan, Italy
Oct 24, 2024 9:45 AM

• Workshop page

BigWarp is an intuitive tool for non-linear manual image registration that can scale to terabyte-sized image data. In this

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/**
	 * Reads a {@link DataBlock} from an {@link InputStream}.
	 *
	 * @param in
	 * @param datasetAttributes
	 * @param gridPosition
	 * @return
	 * @throws IOException
	 */
	@SuppressWarnings("incomplete-switch")

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	public T getValidateDefault(String parameter, Predicate<T> validator, T defaultValue) {
		return getOptional(parameter).filter(validator)
				.map(x -> {
					allDefault = false;
					return x;
				}).orElse(defaultValue);
	}

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#@ File(styles="both") root
#@ String(value="/") datasetPath

/*
 * If you used Fiji to export a multi-scale image with N5Viewer metadata using average downsampling
 * between approximately March 13 and April 15 2024, the translation metadata may be incorrect.
 * 
 * Running this script will correct the metadata.
 * 
 * John Bogovic

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#@ File(styles="both") root
#@ String(value="/") datasetPath

/*
 * If you used Fiji to export a multi-scale an image with COSEM metadata using average downsampling
 * between approximately March 13 and April 15 2024, the translation metadata may be incorrect.
 * 
 * Running this script will correct the metadata.
 * 
 * John Bogovic

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#@ File(styles="both") root
#@ String(value="/") datasetPath

/*
 * If you used Fiji to export a multi-scale OME-Zarr image using average downsampling
 * between approximately March 13 and April 15 2024, the translation metadata may be incorrect.
 * 
 * Running this script will correct the metadata.
 * 
 * John Bogovic

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#@ DatasetService ds
#@ UIService ui
#@ Long radius = 13
#@ String (choices={"Diamond", "Hypersphere"}, style="listBox") shapeType

/*
 * Displays a Diamond or Hypersphere neighborhood for a given radius
 */
if( shapeType.equals("Diamond"))
	shp = new DiamondShape(radius);

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package org.janelia.saalfeldlab.n5.generateExamples;

import org.janelia.saalfeldlab.n5.Bzip2Compression;
import org.janelia.saalfeldlab.n5.Compression;
import org.janelia.saalfeldlab.n5.GzipCompression;
import org.janelia.saalfeldlab.n5.Lz4Compression;
import org.janelia.saalfeldlab.n5.N5Writer;
import org.janelia.saalfeldlab.n5.RawCompression;
import org.janelia.saalfeldlab.n5.XzCompression;
import org.janelia.saalfeldlab.n5.blosc.BloscCompression;