Object Tracking (Octave)

Description

Nuclei tracking in 2D time-lapse with Octave tracker (adapted from Matlab LOBSTER version.

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NucleusJ

Description

Quote

Starting from image stacks, the nuclear boundary as well as nuclear bodies are segmented. As output, NucleusJ automatically measures 15 parameters quantifying shape and size of nuclei as well as intra-nuclear objects and the positioning of the objects within the nuclear volume.

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Nuclei Segmentation (ilastik)

Description

NEUBIAS-WG5 workflow for nuclei segmentation using ilastik v1.3.2 and Python post-processing.

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Nuclei Segmentation (CellProfiler)

Description

This workflow processes a group of images containing cells with discernible nuclei and segments the nuclei and outputs a binary mask that show where nuclei were detected. It was developed as a test workflow for Neubias BIAFLOWS Benchmarking tool.

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Nuclei Tracking (ImageJ)

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Nuclei Segmentation (Python)

Description

This workflow processes images of cells with discernible nuclei and outputs a binary mask containing where nuclei are detected.

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Nessys

Description

Nessys: Nuclear Envelope Segmentation System

 

Nessys is a software written in Java for the automated identification of cell nuclei in biological images (3D + time). It is designed to perform well in complex samples, i.e when cells are particularly crowded and heterogeneous such as in embryos or in 3D cell cultures. Nessys is also fast and will work on large images which do not fit in memory.


Nessys also offers an interactive user interface for the curation and validation of segmentation results. Think of this as a 3D painter / editor. This editor can also be used to generate manually segmented images to use as ground truth for testing the accuracy of the automated segmentation method.


Finally Nessys, contains a utility for assessing the accuracy of the automated segmentation method. It works by comparing the result of the automated method to a manually generated ground truth. This utility will provide two types of output: a table with a number of metrics about the accuracy and an image representing a map of the mismatch between the result of the automated method and the ground truth.

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FISHfinder

Description

Quote:

Fluorescence in situ hybridization (FISH) is used to study the organization and the positioning of specific DNA sequences within the cell nucleus. Analyzing the data from FISH images is a tedious process that invokes an element of subjectivity. Automated FISH image analysis offers savings in time as well as gaining the benefit of objective data analysis. While several FISH image analysis software tools have been developed, they often use a threshold-based segmentation algorithm for nucleus extraction. As fluorescence signal intensities can vary significantly from experiment to experiment, from cell to cell, and within a cell, threshold based segmentation is inflexible and often insufficient for automatic image analysis, leading to additional manual extraction and potential subjective bias. To overcome these problems, we developed a graphical software tool called FISH Finder to automatically analyze FISH images that vary significantly. By posing the nucleus extraction as a classification problem, compound Bayesian Classifier is employed so that contextual information is utilized, resulting in reliable classification and boundary extraction. This makes it possible to analyze FISH images efficiently and objectively without adjustment of input parameters.

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Measure distance of organelles from nucleus in 3D

Description

A simple workflow is described in the following for measuring subcellular localizations of organelle by the distance from the nucleus. For example, you can quantify how far some type of vesicles or protein aggregates are apart from the nucleus border. This workflow is for analyzing 3D data.

Data requirements:

  • 3D data, 2 channels
  • Channel 1: nucleus stain = Channel 2: stain for marker you want to quantify the distance to nucleus for

Workflow:

  1. Nucleus detection: Imaris

- Add a new SURFACE object, name it "nuclei" - Follow the object detection wizard to segment nucleus objects

  1. Marker object detection: Imaris

- Add a new SURFACE object - Follow the object detection wizard to segment nucleus objects

  1. Creating of distance map channel: Imaris

- In the image processing menu, go to SurfacesFunctions>>Distance Transformation

  1. MATLAB:

- select nucleus objects and "distance outside objects" - A new image channel should be created now by the Matlab script

  1. Distance measurement
  • The generated distance map channel represents the distance from the nucleus border in pixel values. Thus, the distance of an organelle from the nucleus is equivalent to its mean gray value of the distance map channel.
    For distance measurement, just export the mean gray value of the distance channel for each object.

** Please note:**
In the described workflow, the distance is always calculated to the closest nucleus border. This could be also the nucleus of a neighboring cell, which generates some error. A more complex approach to avoid this error would incorporate a cell segmentation step to assign certain organelle objects to certain cells. Therefore, a cell region marker is needed.

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Find cells using nuclear and membrane fluorescence

Description

This protocol first extracts the cell nuclei from a given fluorescence channel (full labeling), and grows a contour from each nucleus to extract the cell edge in another fluorescence channel (membrane-labeling).