trasse

## SkeletonToGraph.ipynb

      
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                trasse
                / SkeletonToGraph.ipynb
            
            
              Created
              February 11, 2020 07:55
                — forked from jeanpat/SkeletonToGraph.ipynb
            
              
                A ipython notebook. Takes an image, converts its skeleton to a networkx graph
              
          
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## !Coding helper scripts for QuPath
Collections of scripts harvested mainly from Pete, but also picked up from the forums
If you are starting with 0.2.0m4+ START HERE: https://petebankhead.github.io/qupath/2019/08/21/scripting-in-v020.html

TOC

Coding-List methods for object.groovy - Select an object, see what functions work for it.

Edit metadata.groovy - Add pixel values and maginification (and possibly other things). Shouldn't be necessary after m3

Efficiently collecting objects.groovy - More efficient scripting

## QuPath-Import binary masks.groovy
/**
 * Script to import binary masks & create annotations, adding them to the current object hierarchy.
 *
 * It is assumed that each mask is stored in a PNG file in a project subdirectory called 'masks'.
 * Each file name should be of the form:
 *   [Short original image name]_[Classification name]_([downsample],[x],[y],[width],[height])-mask.png
 *
 * Note: It's assumed that the classification is a simple name without underscores, i.e. not a 'derived' classification
 * (so 'Tumor' is ok, but 'Tumor: Positive' is not)
 *

## Dockerfile
########################################################################################
# Dockerfile to build cytopacq which allows to simulate fluorescence microscopy images
# Based on Ubuntu
########################################################################################
#
# Register under http://cbia.fi.muni.cz/registration-form.html
# and download the files sim-app.tgz and i3dcore_and_i3dalgo.zip from
#   http://cbia.fi.muni.cz/download.php?dl=sim-app.tgz and
#   http://cbia.fi.muni.cz/download.php?dl=i3dcore_and_i3dalgo.zip
# Put the two files and this Dockerfile into the same folder. In a shell
	Collections of scripts harvested mainly from Pete, but also picked up from the forums
	If you are starting with 0.2.0m4+ START HERE: https://petebankhead.github.io/qupath/2019/08/21/scripting-in-v020.html

	TOC

	Coding-List methods for object.groovy - Select an object, see what functions work for it.

	Edit metadata.groovy - Add pixel values and maginification (and possibly other things). Shouldn't be necessary after m3

	Efficiently collecting objects.groovy - More efficient scripting
	/**
	* Script to import binary masks & create annotations, adding them to the current object hierarchy.
	*
	* It is assumed that each mask is stored in a PNG file in a project subdirectory called 'masks'.
	* Each file name should be of the form:
	* [Short original image name]_[Classification name]_([downsample],[x],[y],[width],[height])-mask.png
	*
	* Note: It's assumed that the classification is a simple name without underscores, i.e. not a 'derived' classification
	* (so 'Tumor' is ok, but 'Tumor: Positive' is not)
	*
	########################################################################################
	# Dockerfile to build cytopacq which allows to simulate fluorescence microscopy images
	# Based on Ubuntu
	########################################################################################
	#
	# Register under http://cbia.fi.muni.cz/registration-form.html
	# and download the files sim-app.tgz and i3dcore_and_i3dalgo.zip from
	# http://cbia.fi.muni.cz/download.php?dl=sim-app.tgz and
	# http://cbia.fi.muni.cz/download.php?dl=i3dcore_and_i3dalgo.zip
	# Put the two files and this Dockerfile into the same folder. In a shell