bogovicj

#!/bin/bash
#
# Runs the 'claude-dev' docker image for claude, mounting a set of volumes
# into the container. Folders are mounted into the /workspace folder.
#
# All arguments are mounted. If no arguments are provided, the current working directory is mounted.

args=""
if [ $# -eq 0 ]
then

bogovicj

#!/usr/bin/env bash

## Which benchmark to run 
## BlockReadWriteBenchmarks : benchmarks file reading and decoding
## BlockCodecBenchmarks"    : benchmarks decoding only 
benchmark="BlockCodecBenchmarks"

## Benchmark parameters
dataTypes="int32"
fillType="random"

bogovicj

#@ File f
#@ UIService ui
#@ IOService io

/**
 * Explicitly use the ImageJ2 IOService to open some file.
 */
ui.show(io.open(f.getAbsolutePath()));

bogovicj

n5 = new N5Factory().openReader("/home/john/tmp/mitosis.zarr");
println(n5.getClass());

node = N5DatasetDiscoverer.discover(n5);
println(node.printRecursive());
println(node.getDescendant("s0").get().getMetadata().getClass());

import org.janelia.saalfeldlab.n5.N5Reader;
import org.janelia.saalfeldlab.n5.ij.N5Importer;

bogovicj

n5 = new N5Factory().openReader("/home/john/tmp/mitosis.zarr");
println(n5.getClass());

node = N5DatasetDiscoverer.discover(n5);
println(node.printRecursive());
println(node.getDescendant("s0").get().getMetadata().getClass());

import org.janelia.saalfeldlab.n5.N5Reader;
import org.janelia.saalfeldlab.n5.ij.N5Importer;

bogovicj

#!/bin/bash

function initialize() {

    # Make sure the guard is oriented to the right
    #
    # I happen to know that the guard is oriented up for my input
    # So the commands below do a clock-wise rotation
    # (this would be easy enough to generalize)

bogovicj

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

bogovicj

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

bogovicj

bogovicj

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