Commit 45882793 by walker

parents
.gitignore 0 → 100644
 .DS_Store \ No newline at end of file
 # Course Material Image Analysis This repo contains the slides of the 3 day course on image analysis which was given by the CBG Scientific Computing Facility(SCF) / Scionics online in 2020-12. For course material of our other courses + further resources check [here](https://git.mpi-cbg.de/scicomp/bioimage_team/coursematerialimageanalysis). ### Course overview * Day 1: Introduction to image analysis * Image basics: What is an image, visualization, histograms, measurements * Counting objects (spot detection) * Segmentation 1: classic segmentation pipeline * Day 2: Image segmentation (continued) * Image filters, morphological operations * Segmentation 2: pixel classification (machine learning) * 3D data & visualization * Good practices * Day 3: ImageJ / Fiji Automation and Macro Language * ImageJ macro language basics * Processing an image with a macro * Batch processing ### License The content of this repository is licensed under Creative Commons Attribution-NonCommercial 4.0 International License (CC BY-NC). To view a copy of this license, visit .
 // intialize program v = newArray(3, -4, 0); animals = newArray("dog", "cat", "mouse"); // access first element of array first_element = v[0] print("First element of v = " + first_element); // concatenate the 2 arrays merged = Array.concat(v , animals); // print using Array.print print("This is a concatenated array =") Array.print(merged); // create a mixed array mixed = newArray("cell", 2, 8, "nucleus"); print("This is a mixed array =") Array.print(mixed); // start typing 'Array.' to discover more functions \ No newline at end of file
 // This program is our second example. // It sums up two numbers. // // Usage: // * Run it in FIJI (www.fiji.sc) // // Author: Robert Haase, MPI CBG, // rhaase@extern.mpi-cbg.de // July 2016 // initialise program a = 1; b = 2.5; // run complicated algorithm final_result = a + b; print( final_result );
 // initialise program // operator '=' is used to assign values to variables n1 = 3; n2 = 2.5; n3 = 4; // operator '+' can add values stored into variables sum = n1 + n2 + n3; // compute mean of the 3 numbers mean = sum / 3; // show the results print("Sum =") print(sum); print("Mean =") print(mean) // operator '+' can directly add values as well sum_new = 4 + 5; // show the results print("New sum ="); print(sum_new);
 // initialize program firstname = "Robert"; lastname = "Haase"; // here opertator '+' is used to concatenate or join strings // " " is for space between strings name = firstname + " " + lastname; another_name = "Max " + "Mustermann"; // show results print("Hello " + name); print("Hi " + another_name);
 // initialize program n1 = 3; n2 = 2.5; n3 = 4; // compute sum and meam sum = n1 + n2 + n3; mean = sum / 3; // use '+' to concatenate and print nice results // observe the difference in output with and without spacing print("Input numbers = " + n1 + ", " + n2 + ", " + n3); print("Without spacing:"); print("sum=" + sum); print("mean=" + mean) print("With spacing:") print("sum = " + sum); print("mean = " + mean)
 // initialise program firstname = "Robert"; lastname = "Haase"; cellname = "cell-10" // show the result print(firstname); print(lastname); print(cellname);
 // initialise program a = 1; b = 2.5; // run complicated algorithm final_result = a + b; // show the result print(final_result);
 Sentence = "Can you can a can as a canner can can a can?"; if (startsWith(Sentence, "Can") { print(sentence); } \ No newline at end of file
 a = 5; b = 7; sum = a + b; ratio = a / b; print("The sum is + sum); print("The ratio is " + ratio);
 // get current image title imageName = getTitle(); // get image statistics getStatistics(area, mean, min, max, std); // show results print("Image name is " + imageName); print("The grey value ranges from " + min + " to " + max + ". "); print("It has an average of " + mean + " +- " + std + ". "); close();
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