Semi-automated

An exponential curve fitting library used for Fluorescence Lifetime Imaging (FLIM) and Spectral Lifetime Imaging (SLIM), available as:

• Source code as C/C++ and Java library

• ImageJ plugin

• Standalone Open-Source Windows application

Publications:

• Barber, P.R., Proc. SPIE, 5700, 2005.pdf
• Barber, P.R., J. R. Soc. Interface, 6, 2009.pdf

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

Particle detection is based on "Analyze Particles" in ImageJ. It probably could also be used in spot detection, not limited to centromere.

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), Developmental Cell 40, 104–113,
• Guo et al. (2017) Nature Communications volume 8, Article number: 15775 (2017) doi:10.1038/ncomms15775
• Lgosdon et. al. (2015) J Cell Biol Mar 2015, 208 (5) 521-531; DOI: 10.1083/jcb.201412011
• Bodor et al. (2014), eLife. 2014; 3: e02137

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.

ITK-SNAP is a software application used to segment structures in 3D medical images. It can also be used as a 3D annotation tool for deep learning. It is based on ITK, VTK libraries.