Create Measurement tool for OMERO.insight.

[donald]

OMERO.insight needs to allow users to quantify the results of experiments.

All values should be shown in a grid which will be user editable (JTable), and then exportable to excel(CVS), other formats(XML?).

Any method which has a change in time, or z section should have, if possible, a graph method associated with it, so that the user can see at a glance the change in the values.

All measurements should be able to be shown in pixels and microns.

Initially type could be specified simply by the colour of the object.

Geometry

The user should be able to create a set number of primitives and display them on the screen, they should be able to pick them, move them and change their properties. Later a method for propagating the objects through z, and t sections will be required.

• Points should only represent the individual pixels in an image, though they may be larger than one pixel for display purposes.
• Size
• Colour
• Lines
• Thickness the line then covers an area of the image.
• Colour
• Area
• N-point polygons
• Colour

Measure values in an area or point.

• Individual point
• On image
• In lens zoom window
• Area
• Simple stats: Average intensity, min/max, etc.
• Show change in values over time (total, average, geometric mean, etc.)
• Display, graph.
• Texture analysis
• Seems to give good indication of cell stage(phenotype?)
• Line
• Line graph of values
• Simple stats
• Show change in values over time
• Display, graph

Distance measurements

• Points
• Distance between points
• Points to be labeled, across z, t sections.
• Track distance between sets of points
• Track distance z, t sections for points.
• Calculate total distance between sets of points.
• Lines
• Length of line
• Angle from x-Axis
• Angle between 2 lines
• Area
• Size of area

Counting

• Points
• Assign a point a type.
• Count number of types
• Count change of types over t, z sections
• Areas
• Assign an area a type
• Count number of areas
• Count size of areas, by type
• Show changes in area by type of time

Graphing

• Generating simple histograms from data
• Binning of objects
• Intensity. Area
• Line and surface plots
• Initially fixed axis

Segmentation

• Integration of segmentation tools to generate points, areas
• Initially only try cellprofiler, later provide interface so other tools can be used.

Analysis

• Track points
• User assigns class to object and the tool will analyse movement, change. The result of the analysis will be graphed, displayed in a grid which can be exported to excel.
• Optical flow, this should be able to track the movement of the cells, (other objects) over time.
• Change analysis, calculation of stats from the change.
• Texture analysis
• Simple algorithm could give a user the ability to click a few points (cells) and then let the algorithm try and pre-assign the rest of the cells.
• Specifically for cell stage