2D

ijblob

Component
Description

## Features >The IJBlob library indentifying connected components in binary images. The algorithm used for connected component labeling is: >Chang, F. (2004). A linear-time component-labeling algorithm using contour tracing technique. Computer Vision and Image Understanding, 93(2), 206–220. doi:10.1016/j.cviu.2003.09.002 ##Reference Wagner, T and Lipinski, H 2013. IJBlob: An ImageJ Library for Connected Component Analysis and Shape Analysis. Journal of Open Research Software 1(1):e6, DOI:

has topic
Bioimage informatics
has function
Object detection
Object feature extraction
Shape features
need a thumbnail

Counting Clumped Cells

Workflow
Description

A workflow combining ImageJ macro and manually using Trainable Weka Segmentation plugin for counting clumped cells.

has function
Cell segmentation
Object counting

Histo_surfaces

Workflow
Description

An ImageJ macro for calculating empty surfaces on histological slices (ex: tubules in a kidney).

has topic
Digital histology

Centromere Recognition and Quantification

Workflow
Description
<p>Particle detection is based on "Analyze Particles" in ImageJ. It probably could also be used in spot detection, not limited to centromere. &gt;This macro is described in Bodor et al. (2012). The macro recognizes centromere or kinetochore foci in Delta Vision or TIFF images and determines their centroid position. Fluorescent intensities are then measured for each centromere by placing a small box around the centroid position of the centromere. The peak intensity value within the box is corrected for local background by subtraction of the minimum pixel value. This process results in an accurate measurement of large numbers of centromere or kinetochore-specific signals. Following papers uses CRaQ (picked up, maybe more): - [Fachinetti et al. (2017)](https://www.cell.com/developmental-cell/pdf/S1534-5807(16)30909-1.pdf), Developmental Cell 40, 104–113, - [Guo et al. (2017)](https://www.nature.com/articles/ncomms15775) Nature Communications volume 8, Article number: 15775 (2017) doi:10.1038/ncomms15775 - [Lgosdon et. al. (2015)](http://jcb.rupress.org/content/208/5/521) J Cell Biol Mar 2015, 208 (5) 521-531; DOI: 10.1083/jcb.201412011 - [Bodor et al. (2014)](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4091408/), eLife. 2014; 3: e02137</p>
has topic
Fluorescence microscopy
has function
Spot detection

Orthogonal Views (ImageJ)

Component
Description

A menu item in ImageJ that allows you to inspect a 3D stack with orthogonal views (XY, XZ, YZ planes). Slicing plane could be interactively moved by dragging crosses. Pedro Almada wrote a plugin to save the current orthogonal views as montage. ## ImageJ Macro Usages [Save orthogonal views | OrthoSaver](http://uic.igc.gulbenkian.pt/macros/OrthoSaver.ijm) >ImageJ's orthogonal viewer for 3D stacks doesn't let you easily save the current orthogonal view. This macro, once installed, lets users create a montage with the currently open orthogonal views and selection guides. To use it, open an image z-stack and open the orthogonal viewer. With the mouse, choose which are the sections of interest to you and without moving the mouse, press F2. You'll get a montage of the currently selected orthogonal view.

has topic
Bioimage informatics
has function
Image visualisation
need a thumbnail
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