QuantiFish is a quantification program intended for measuring fluorescence in images of zebrafish, although use with images of other specimens is possible. This package is geared towards analysis of fluorescent infection models. The software is designed to automate processing of images of single fish, and outputs results as a .csv file. Alongside measures of total fluorescence above a threshold, this package also introduces several measures for dissemination and distribution of fluorescence throughout the specimen.
clij is an ImageJ/Fiji plugin allowing you to run GPU-accelerated code from within Fijis script editor (e.g. macro and jython). CLIJ is based on ClearCL, Imglib2 and SciJava. It contains components for image filtering, thresholding, spatial transforms, projections, binary image processing and basic signal measurements.
3-D density kernel estimation (DKE-3-D) method, utilises an ensemble of random decision trees for counting objects in 3D images. DKE-3-D avoids the problem of discrete object identification and segmentation, common to many existing 3-D counting techniques, and outperforms other methods when quantification of densely packed and heterogeneous objects is desired.
The Image "Pos22" is taken from the dataset idr0040-aymoz-singlecell/experimentA/YDA306_AGA1y_PRM1r_Mating. It is a timelapse Image with 42 timepoints separated by 5 minutes. This Image is used to fit a model for the growth of the yeast cells. The notebook does not replicate any of the analysis of the above mentioned paper.
Its purpose is mainly to demonstrate the use of Jupyter, rOMERO-gateway and EBimage.
What it does:
For each time point of one movie:
Read the image for this time point from the IDR
Threshold the images and count the cells using EBimage functions
Fit an exponential model to the count of cells against time to get a coefficient of grow (exponential factor)