Modules

Analysis modules

PickCells supports the following analysis modules:

Name	Icon	Description	Tags
Basic Segmentation		Identify individual objects in images using basic segmentation operations such as thresholding and morphological filtering.
Boundary Extractor		Extract distinct boundaries in a segmented image. Boundaries are sections of the contour of objects where the object is touching either the background of the image, the border of the image, or other objects e.g. between cavities and surface. Extracting these bounaries allows them to be used as landmarks for further analysis of the topology of a sample.
Clustering		Use the DBScan algorithm to cluster objects in space.
Intrinsic Features		Compute intrinsic features of images, particularly segmented shapes, for example intensities or volumes.
Mitosis Detector		Identify Mitosis events in images.
Neighbours Identifier		Create links between adjacent objects. The maximum distance between adjacent objects and the maximum variation allowed in the distance between neighbouring objects can be selected. The distance and contact area between objects will be stored in the created links. A vector identifying the center of mass of the neighbourhood will also be computed.
NESSYs: Nuclear Envelope Segmentation SYstem		Automatically identify cell nuclei in biological images (2D - 3D - 3D + time). 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.
Network Analysis		Run a basic network analysis. Given a type of link accessible from Images which connects objects of the same type, compute the degree of each node, the average degree of neighbouring nodes at depth 1 and 2, as well as the local clustering coefficient for each node.
Nuclei Centrosomes Assignment		Automatically associate nuclei with centrosomes. This module tries to maximize the number of cells with 1 or 2 centrosomes, but will allow nuclei to have more than 2 centrosomes. A basic classification of the cells is then performed to identify mitotic versus interphase cells versus cells with centrosome amplification.
Object Tracker		Track objects, allowing for divisions, missing objects over several frames and object disappearance.
Overlap (Membership) Finder		Create relationships between segmented objects if their labels overlap. The vector indicating the orientation towards the barycenter of the target is also computed. This can be used, for example, to determine if a specific nucleus belongs to a specific structure.
Relative Connector		Calculate relative positions between source objects and a closest target object. These are recorded as connections of type “RELATIVE_TO”. A vector for the direction and an anchor point in the mesh of the source and target object is also computed.
Segmentation Editor		View and edit segmentation results. View an image with an overlap containing the boundaries of segmented shapes within a segmentation result, correct the segmentation and quantify its accuracy. The number of edits is recorded in a SegmentationResult object.	segmentation, editor
Segmented Object Comparator		Creates “BEST MATCH” between segmented objects if their labels overlap by more than 50%. Key differences between the shapes are also computed.
Spots Detector		Identify bright spots in images, including noisy images, based on the difference of a Gaussian filter.
Spots Editor		View an image with an overlay containing the location of detected spots and correct and quantify the accuracy of the original detection. The number of edits is stored in the corresponding Image node in the database.

Visualisation modules

PickCells supports the following visualisation modules:

Name	Icon	Description	Tags
2D Scatter (Bubble) Plot		Create a 2D scatter (bubble) plot.
3D Directional Plot		Create a 3D directional plot.
3D Scatter Plot		Create a 3D scatter plot.
3D Scene		Display a 3D scene data, if the data can be rendered in 3D.
Histogram		Create a histogram.
Image		Load and view a specific image and select objects in the image.
Pie Chart		Create a pie chart.
Polar Plot		Create a polar plot (rose diagram) to display the distribution of angular data.
Time Series Plot		Create a time series plot.
Track Editor		View and edit tracking outputs.
Tree View		Display trees for Series Generators.