lacan

/*
 * Simple bissection tool. By Olivier Burri at the BioImaging and Optics Platform
 * Provided as-is based on a request of the ImageJ Forum: http://forum.imagej.net/t/how-do-you-measure-the-angle-of-curvature-of-a-claw
 * 
 * Mouse listening code based on imageJ example
 * https://imagej.nih.gov/ij/macros//GetCursorLocDemo.txt
 * 
 * To install, use 'Plugins > Macros > Install...' and select this file
 * 
 * To run, create a line selection and press F2.

ctrueden

package net.restlesscoder.sandbox.imagej;

import io.scif.FieldPrinter;
import io.scif.Format;
import io.scif.Metadata;

import net.imagej.ImageJ;

public class ParseMetadata {

lacan

/*
 * Simple script that takes a selection and computes the curvature radius for the whole perimeter of the shape.
 * 
 * By Olivier Burri, 
 * BioImaging and Optics Platform, BIOP
 * Ecole Polytechnique Fédérale de Lausanne (EPFL)
 * Last update: May 2017
 * 
 * 
 */

naupaka

# function to do a dodged half-boxplot and jittered points next to each other
#
# data_in should be a data frame
# factor_col should be a bare column name (not a string)
#     although it will work if that column is factor or a character type
# numeric_col is the y axis continuous variable
# offset is the width of the boxplots and jittered point cloud
#
# the basic approach is to draw a boxplot without the tails
#   (e.g. only the interquartile range) and then use segments to add the

ctrueden

#@ ConvertService convert
#@ ImagePlus imp

import bdv.util.BdvFunctions
import bdv.util.BdvOptions

import ij.gui.Overlay
import ij.gui.Roi

import net.imglib2.roi.Masks

bogovicj

#@Dataset(label="Image to transform") img
#@Double(label="scale") scaling_factor
#@UIService ui

import net.imglib2.*;
import net.imglib2.realtransform.*;
import net.imglib2.view.*;
import net.imglib2.interpolation.*;
import net.imglib2.interpolation.randomaccess.*;

ctrueden

#@dependency(group="org.boofcv", module="boofcv-core", version="0.33")
#@dependency(group="org.boofcv", module="boofcv-swing", version="0.32")

#@both ImagePlus imp
#@output ImagePlus (label="Watersheds") watersheds
#@output ImagePlus (label="Regions") regions
#@output ImagePlus (label="Seeds") seeds

import boofcv.alg.filter.binary.BinaryImageOps
import boofcv.alg.filter.binary.ThresholdImageOps

ctrueden

#!/usr/bin/env python

#
# scifio.py - Open images as numpy arrays using SCIFIO and Bio-Formats.
#

# -- Settings --

max_mem_mb = '6144'
scifio_lifesci = False

bobpeers

#prefect imports
import prefect
from prefect import task, Flow
from prefect.schedules import Schedule
from prefect.schedules.clocks import CronClock
from prefect.storage import Local
import pendulum
import knime
import os