Cell counting is an indispensable and essential problem because it directly affects the efficiency of many cell-based gene expression systems like Baculovirus Expression Vector System (BVES). Traditionally, this task is usually performed by microscopic-based counting. For example, the Neubauer, Burker and Fuchs-Rosenthal chambers are well known methods for counting cells in different cell concentration of interest. However, all of these methods have to be manually manipulated and therefore are prone to cause errors for the same person or different persons. Furthermore, most of them require frequent repetitions for validations.
Performs crowd-based images annotation. Quanti.us is a portal that assists users in recruiting groups of untrained Mechanical Turk workers (Turkers) to annotate images using a set of interaction tools. The platform enables uploading of image sets, selection of an analysis tool, and provides sets of instructions. Users can gather hand annotations by marshaling paid Turkers to annotate a range of image types. Quanti.us thus makes crowd analysis of scientific images applicable to several annotation problems.
Determines real cell size distributions in a tissue from cross-section images. EstiTiCS can correct for three types of bias that are inherent to cell size measurements from cross-section images. It was applied to adipocyte size measurements during a weight-loss intervention study. This tool aims to estimate the real cell size distribution based on cross-sectional measurements with a maximum-likelihood approach.
Allows automatic segmentation through an interactive interface. AutoCellSeg enables researchers to select object features for supervised image segmentation method. This method uses multi-thresholding aided by a feedback-based watershed algorithm taking segmentation plausibility criteria into account. Moreover, this program integrates an algorithm that automatically segments the colonies from the unwanted background in a way that colony forming unit (CFU) boundaries are obtained.
Allows quantification of Drosophila egg laying. Quantifly automates egg counting after a brief training period. The software consists of a baseline algorithm with the bias correction, along with a regions of interest (ROI) labelling interface. Users are required to train the algorithm by identifying eggs within a few ROIs on several exemplar images, and, then, the software uses the model trained to detect eggs in a batch of images.
Allows users to detect and count fluorescent signals in microscopy images of cells. Blob Finder is a free software that performs two types of analysis: (i) an average count, for quantifying the number of nuclei and signals in an image; (ii) and a single cell analysis, that assigns each signal to the closest cell and get a signal count for each cell in the image. It also performs on-z_stacks of the cell with a maximum projection to project the image data into a 2D image.
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