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Volker edited this page Sep 22, 2020 · 33 revisions

Welcome to the imagej_macros_and_scripts wiki! You can find a pdf-snapshot of the wiki here.

MRI ImageJ-macros

ImageJ Macro Tool Sets for Biological Image Analysis

Biological Image Analysis Toolsets

  1. 3D_Nuclei_Clustering_Tool
    Analyze the clustering behavior of nuclei in 3D images. The centers of the nuclei are detected. The nuclei are filtered by the presence of a signal in a different channel. The clustering is done with the density based algorithm DBSCAN. The nearest neighbor distances between all nuclei and those outside and inside of the clusters are calculated.

  2. Adipocytes Tools
    The Adipocytes Tools help to analyze fat cells in images from histological section.



  3. MRI_Analyze_Alignment_of_Muscles_Tool
    The tool uses the Directionality plugin to measure the main direction of the structures in the image and the dispersion. It is used in this context to analyze to which degree the muscles in the image are vertically aligned. The tool allows to run the Directionality plugin in batch-mode on a series of images. The direction-histograms and the measurements are exported as csv-files.
  4. Analyze_Calcium_Signals_In_Spines
    Analyze calcium signals in dendritic spines. The images consist of time-series of calcium signals. Each image contains a selection that marks the point of stimulation. The tool finds the region to analyze close to the point of stimulation. It measures the intensity of the calcium signal in the whole region of interest and in the segmented spots.
  5. Analyze_Cardiomyocytes
    Analyze images from second harmonics microscopy of cardiac muscle cells (cardiomyocytes). The tool measures the length of the sarcomeres using the FFT of the image and the degree of organization of the sarcomeres by using the dispersion provided by the Directonality command of FIJI. Although the input images can be stacks only the middle slice is used for the analysis.
  6. Analyze_Complex_Roots_Tool
    This tool allows to analyze morphological characteristics of complex roots. While for young roots the root system architecture can be analyzed automatically, this is often not possible for more developed roots. The tool is inspired by the Sholl analysis used in neuronal studies. The tool creates a binary mask and the Euclidean Distance Transform from the input image. It then allows to draw concentric circles around a base point and to extract measures on or within the circles. Instead of circles, which present the distance from the base point, horizontal lines can be used, which present the distance in the soil from the base-line.
  7. Analyze Spheroid Cell Invasion In 3D Matrix
    The tool allows to measure the area of the invading spheroïd in a 3D cell invasion assay. It can also count and measure the area of the nuclei within the speroïd.


  8. Analyse Spots Per Protoplast
    The tool counts the spots per protoplast. If a third channel is provided it is used to filter out detected protoplasts that do not have exactly one nucleus.


  9. Arabidopsis Seedlings Tool
    The Arabidopsis Seedlings Tool allows to measure the surface of green pixels per well in images containing multiple wells. It can be run in batch mode on a series of images. It writes a spreadsheet file with the measured area per well and saves a control image showing the green surface that has been detected per well.

  10. Cluster Analysis of Nuclei Tool
    Analyze the clustering behavior of nuclei in DAPI stained images. The nuclei are detected as the maxima in the image. Using a threshold intensity value, maxima below the threshold are eliminated. The resulting points are clustered using the DBSCAN algorithm. The nearest neighbor distances between all nuclei, and those outside and inside of the clusters are calculated.
  11. Count Axonal Projections Tool
    Count the number of axonal projections that cross a given line. The tool detects and counts the maxima along a line-selection, for example a segmented line.


  12. MRI_Count_Spot_Populations_Tool
    The tool detects and and counts the spots (or blobs) in an image. It has been created for the counting of bacteria colonies in in Petri-dishes. It separates the spots into two populations and counts each population individually. The populations are separated by the area of the spots. The tool uses expectation maximisation clustering from the weka software.
  13. MRI_Create_Synthetic_Spots_Tool
    The tool creates images of 2D-spots for the evaluation and benchmarking of spot detection tools. Two populations of spots with different means and variations of the size can be created in the same image.


  14. MRI_Fibrosis_Tool
    Measure the relative area of sirius red stained fibrosis. The tool uses the colour deconvolution plugin from Gabriel Landini.


  15. FLIM FRET_Volume_Tool
    The tool measures in FLIM-FRET images, for each cell, the total volume of the cell and the volume occupied by values in a given range. It displays the positions of the values in the range in a result image.


  16. Foci-Per-Nucleus-Tool
    The tool detects, counts and measures the foci per nucleus. It reports the number of small, medium sized and big fosci per nucleus. It also measures the area and mean intensity of the nuclei.


  17. MRI_Heights_of_Surfaces_Tools
    The tools help to compare the height in the z-dimension of the signals in different channels. It calculates the heights normalized by the maximum height in a reference channel. Only places where the signal is not zero and the reference channel maximal are taken into account.

  18. Intensity Per Nucleus Tool
    The tool segments the nuclei in the dapi or hoechst channel of the image and measures the mean intensity per nuclei in the other channels of the image. The macro can be applied recursively to all images in a folder and its subfolders.

  19. Intensity Ratio Nuclei Cytoplasm Tool
    The tool calculates the ratio of the intensity in the nuclei and the cytoplasm. It needs two images as input: the cytoplasm channel and the nuclei channel. The nuclei channel is used to segment the nuclei. The measurements are made in the cytoplasm channel after the background intensity has been corrected.

  20. Phase Contrast Cell Analysis Tool (Trainable WEKA Segmentation)
    The tool allows to segment cells in non fluorescent microscopy images using the trainable WEKA segmentation. It allows to run a preprocessing that crops and converts images, to apply a classifier created with the Trainable Weka Segmentation plugin to a folder containing images and to open the images in a folder as a stack in the "Trainable Weka Segmentation plugin" to create a classifier.
  21. MRI_Plot_Tool
    Calculate the first derivative of a plot and the zero-crossings of the derivate.



  22. Positions_In_Cell_Tool
    Measure the distance of the accumulation of the molecule in the green channel to the centre of the cell and to the centres of the nuclei. The input image is a z-stack that has the nuclei stained in one channel and the molecule of interest in another channel. The tool finds the central slice of the central cell. It assumes the central slice to be the one on which the surface of the nuclei is maximal, without considering slices at the top or button.
  23. MRI_Root_Hair_Tools
    The tool allows to measure the diameter of the root and the density of the root hair.



  24. Track_Microtubules_Tool
    The tool allows to track the ends of fluorescently labelled microtubules, which are becoming shorter and to measure the speed of the movement of each end. It also creates kymograms and plots distance-per-time.


  25. Transfection_Efficiency_Tool
    The tool helps to measure the transfection efficiency. It reports the percentage of transfected cells in the image. It has tools to manually correct the segmented nuclei (merge and split).


  26. MRI_Width_Measurement_Tool
    Measure the width of a gap between cells where the gap is dark and the membranes of the cells or bright.


  27. Wound Healing Tool
    The MRI Wound Healing Tool can be used to analyze scratch assays. It measures the area of a wound in a cellular tissue on a stack of images representing a time-series.


Workflow and Conversion Toolsets

  1. MRI_Convert_Nikon_Andor_To_Hyperstack
    Because of the big size of the images the microscope cuts images along the time dimension into multiple files each with a number of frames. This tool will for each position and wavelength convert the image. It will do a z-projection, concatenate all time-chunks and save the resulting image. The user has to provide the number of slices in the z-dimension. The pixel size and time interval can automatically be set when provided by the user.
  2. MRI_Convert_Opera_To_Hyperstack
    The tool converts images taken with the Opera into hyperstacks. The image names are in the form r02c04f01p01-ch1sk1fk1fl1.tiff where r is the row, c the column, f the field, p the z-position and ch the channel. The tool converts all images in the input folder.
  3. Load-Corresponding-Images
    The tool allows to open for each image a second image with the same name from another folder. It displays the two images next to each other. It provides navigation through the list of images.
  4. MRI_ND_To_Hyperstack
    The tools converts images in the .nd format to ImageJ hyperstacks. The user selects an .nd file. An image can consist of multiple positions, frames, z-slices and channels. Each position is converted into an ImageJ hyperstack and written into a subfolder of the folder containing the input image.
  5. NDPI export regions
    The tool exports rectangular regions, defined with the NDP.view 2 software from the highest resolution version of the image and saves them as tif-files.
  6. MuVi SPIM_Convert_Tools
    The Muvi-SPIM-Convert_Tools help to convert your hdF5 files comming from a MuVi-SPIM setup.



Single Plugin Tools

  1. Discrete_Histogram_Entropy_Tool
    The tool calculates the discrete histogram entropy H(X), where w is the width of the i-th histogram bin and f the frequency of the value xi.
  2. Distance_Between_Minima_Tool
    The tool measures the mean distance between the minima in the profile plot.



  3. Find_and_Subtract_Background_Tool
    The tool finds the background intensity value and subtract it from the current image. It searches for the maximum intensity value around pixels that are below or equal to the minimum intensity in the image plus an offset.
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