#!bash

# Introduction to Anima
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== Image Analysis platform built on top ==
== of pipeline workflow engine Anduril  ==
==      INTENDED FOR DEVELOPERS!        ==
        http://anduril.org/anima

# Why a new platform (for the developers)

    * Increase Usability following
      http://dx.doi.org/10.1038/nmeth.2073 

    * API for several languages directly
    * Software integration: reuse code
        * No reimplementation errors
          due to using original implementation
    * API forces to document inputs, outputs and parameters

    * Published with source code, 3rd party involvement possible
        * http://code.google.com/p/anduril-imaging/
    * Automated testing of components
        * Run at our concurrent testing site
        * "anduril test" command

# Integration
┌─────────────────────────────────────────────────────────┐
│Anima/Anduril runs components as separate processes      │
│                                                         │
│   * Automated parallelization/cluster run               │
│   * Fast reruns by saving all intermediate phases       │
│       * Rapid development                               │
│   * Components in any language                          │
│   * Direct APIs for: Fiji, CellProfiler, Matlab, Python,│
│                      ImageMagick, Bash, Perl, Java, R   │
│       * Basically anything scriptable                   │
├─────────────────────────────────────────────────────────┤
│Ease of analysis                                         │
│   * Integrate analysis with other fields                │
│      Statistics, Machine Learning, Visualization.. etc  │
│   * Abstracts algorithms and methods from analysis flow │
│   * Does not reinvent the wheel:                        │
│      * Standard image formats, CSV files for data,      │
│        PDF, HTML+js for complex visualization           │
│      * Easy to include in publications, web pages       │
└─────────────────────────────────────────────────────────┘

# Typical use

    * Develop new algorithm in your favorite language
    * Use existing tools already in any platform
    * Flow the data with Anima

    * Reuse parts of scripts later!

# Example pipeline
------------------
#!/usr/bin/env anduril-runner

import anduril.builtin._
import anduril.tools._
import anduril.anima._
import org.anduril.runtime._

object Tutorial {
// refer to a directory with images, names prefixed either "case" or "ctrl"
  val source_images=INPUT(path="folder")
// Extract 3rd channel as grayscale PNG
  val gray_dapi=BFConvert(source_images, switches="-channel 0", gray=true)
// Use GraphCut algorithm to create nucleus mask
  val cells=SegmentGraphCut(gray_dapi,minScale=2,maxScale=10)
// Read morphological features from mask
  val features=MorphologyFeatures(cells.mask)
// Split morphological data table to 2 CSV files, by
// 4 first characters of the image file name
  val split_data=CSVSplit(features.out, labelCol="File",
                       regexp="(....)")
// Here, we assume that the 4 first characters were either
// 'ctrl'  or 'case'. Then calculate the t-test on the nucleus areas.
  val t_test=StatisticalTest(matrix=split_data.out("ctrl").force(),
                       matrix2=split_data.out("case").force(),
                       byRow=false,
                       referenceColumns="Area",
                       targetColumns="Area")
// Create a visualization of segmentation. Note that this component is
// independent of many previous ones, and would be run in parallel.
  val visualization=MergeImage(in=makeArray(gray_dapi.out, cells.perimeter), 
                              colors="B,Y")
// Create an HTML web gallery of the visualizations
  val gallery=ImageGallery(inRoot=visualization)
}



# Example with C. Elegans

    * BBBC 10, benchmark data set of 100 images,
      mostly dead / alive worms in an image.
      Annotation at image level.
    * Extract features
    * Calculate Length / end-to-end distance ratio
    * Create classifier
    * 6 minutes on 2-core laptop
    * Pipeline in the supplementary of 
  http://journal.frontiersin.org/Journal/10.3389/fbioe.2014.00025/

# Anima Published
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  http://journal.frontiersin.org/Journal/10.3389/fbioe.2014.00025/
  Anima: Modular workflow system for comprehensive image data analysis. 
  Ville Rantanen, Miko Valori and Sampsa Hautaniemi 
  Front. Bioeng. Biotechnol. doi: 10.3389/fbioe.2014.00025