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This method allows to compute a threshold that preserves the moments of an image. In ImageJ/Fiji, you can access it in Image->Ajust->Threshold and choose Moments in the list. In Aphelion, the tool is in Segmentation->Threshold->AphImgMomentThreshold The original paper is 2449

The QuimP software from Bretschneider group is deployed as ImageJ plugin and includes model-based cell segmentation, cell outline tracking and quantification of the spatially resolved speed of protrusions and retractions. The algorithm to calculate morphological dynamics is faster compared to other approaches (e.g. Machacek and Danuser, 2006). The reference paper describes the workflow for these analyses.

Tracks a cell in a 2D video using active contours, and produces a list of ROI where intensity is measured and reported into a workbook. The cell must be first delineated with a ROI in the first image of the video.

SlideToolkit is a collection of command-line tools to assist with the automated histology analysis of whole-slide images. The publication linked in the "reference" details the actual workflow. 

This includes tools to organize the data, perform tiling and subsequent batch processing of the generated tiles in a cell profiler pipeline. All the tools are designed to run on a single PC or on a HPC system. The scripts in the toolkit are on github under MIT licence.

A utility macro for the specified use of BioFormats plugin. Takes a folder of proprietary images formats (Zeiss zvi, lsm, czi or Nikon nd2) and extracts them to .tif images

The extracted images are located in a folder defined in the menu. Other options: reset spatial scales, reads ROIs, split channels, add stage position in the name.

This protocol computes the optical flow of a 2D+T sequence. The results are displayed with flow arrows painted on top of the original sequence, and also with two additional sequences for the norm of the flow and a color-coded presentation of the flow following the Middlebury convention.

This macro is similar to the LIF_Extractor, but it will output Z-projection of each Z-stack. You can choose the type of projection in addition to the other options. Requires Bio-Formats plugin

Download the protocol,use and modify in Icy. It permits to detect spot with wavelet spot detector block. Input : loop on a folder Outputs: excel, binary, and detection screenshot

This macro extracts .lei and .lif multichannel Z-stacks into multiple .tif stacks, splitting the channels into different stacks. Several options are possible such as background substraction, various filters, or optional reset of spatial scale. Requires Bio-Formats plugin

>OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides). Python and Java bindings are also available. The Python binding includes a Deep Zoom generator and a simple web-based viewer. The Java binding includes a simple image viewer.  

This workflow classifies, or segments, the pixels of an image given user annotations. It is especially suited if the objects of interests are visually (brightness, color, texture) distinct from their surrounding. Users can iteratively select pixel features and provide pixel annotations through a live visualization of selected feature values and current prediction responses. Upon users' satisfaction, the workflow then predicts the remaining unprocessed image(s) regions or new images (as batch processing).

Various ways are proposed in different websites for example:

Requires Matlab Runtime Environment or Matlab. Source code (m-files) are downloaded. Software availability: AVeMap was developed under MATLAB (MathWorks). It is available as an executable, multiplatform program, together with source codes and documentation here, and the source code is also available as Supplementary Software. For practical reasons, this executable version, which does not require MATLAB, runs on a single processor.

Illumination correction is often important for both accurate segmentation and for intensity measurements. This example shows how the CorrectIlluminationCalculate and CorrectIlluminationApply modules are used to compensate for the non-uniformities in illumination often present in microscopy images.

In this example, cells are grown as a tissue monolayer. Rather than identifying individual cells, this pipeline quantifies the area occupied by the tissue sample.

Download package also contains example images. 

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This is a simple example of a DNA damage assay using single cell gel electrophoresis. Here, the measurement of interest is the length and intensity of the comet tail. Also, illumination correction is used to reduce background fluorescence prior to measurement. Also shown is a silver-stained comet example in which the percentage of DNA contained in the tail is calculated.

Example Images: Packaged together with the cellprofiler pipeline file. 

The Leaf Infection Tools allow to measure the area of leaves, of two stainings in different channels and of the overlap region of the two stainings. 

See: http://dev.mri.cnrs.fr/projects/imagej-macros/wiki/Leaf_Infection_Tools

Test image: http://biii.eu/node/1143