HCS images analysis. Define results block

Background

A clear and concise description of what the problem is. Ex. At the moment, Cloud Pipeline does not allow [...] and it would be nice to [...] because [...]

Approach

A new panel shall be added to the HCS preview pop-up. Via this panel, a set of the analysis results to output can be defined. By default, this panel shall have a view like:

The pop-up shall contain:

button to define the images area (plate(s), well(s), etc.) on which the analysis will be performed. By default, this area shall be defined as the current open image or several images (in case, when the whole well is selected)
button to add an output property. By this button, user shall have the ability to add an object property, which will be presented as the separate column in the output spreadsheet
button to add an output property that is defined by the math formula using another property(s)

Define area for analysis

By click the corresponding button, a new pop-up shall appear, e.g.:

This pop-up shall contain several controls to select area for analysis:

plates dropdown list (shown only in case of several plates). By default, the plate of the current image shall be selected. Multiselect is allowed. User can select any plate(s) from the list. If more than one plate is selected - plate and well panels shall become disabled (it means, that all wells and fields of the selected plates shall be automatically selected too)
plate panel with wells. By default, the plate of the current image shall be shown with the current well. User shall have the ability to select one or several wells (first click the well shall select it, second click - unselect). If more than one well is selected - well panel shall become disabled (it means, that all fields of the selected wells shall be automatically selected too)
well panel with fields. By default, the well of the current image shall be shown with the current field(s). User shall have the ability to select one or several fields (first click the field shall select it, second click - unselect)
list of sequences with time points in them. User can select one or several time point in one or different sequences (first click the time point shall select it, second click - unselect)
panel where the currently selected area is described
OK and Cancel buttons

When user selected something - the corresponding fields in the describing panel shall be updated, e.g.:

If no field (and correspondingly, no well and no plate) is selected (excluding case when 'all' fields/wells are selected) - OK button shall become disabled. If no time point in all sequences is selected - OK button shall become disabled.

Add output property

By click the corresponding button, several fields shall appear, e.g.:

Here, the following controls shall appear:

dropdown list with the analysis objects list. Multiselect is not allowed. User shall select an object which property shall be calculated for the output. Near this dropdown list, there should be the remove button that can remove the current object and all its selected properties
dropdown list with the property of the current object. Multiselect is not allowed. User shall select a property which shall be calculated for the output. Near this dropdown list, there should be the remove button that can remove only the current selected property
Add button - to add another property to the current selected object for the output list

Default property for any object shall be "Number of objects", that outputs the count of the selected object. Other properties can be statistic therefore for them, an additional dropdown shall appear while adding, e.g.:

This dropdown list shall include the set of the statistic functions that will be applied for the selected property. Multiselect is allowed. Dropdown list shall include:

Mean - mean value of the property
Median - median value of the property
StdDev - standard deviation
CV % - coefficient of variation (standard deviation divided by mean)
Max - maximum value of the property
Min - minimum value of the property
Sum - summary of all values of the selected property

At least one item in the statistic list shall be selected, there should not be the ability to unselect all items.

Each property from that list shall be calculated and output after the analysis as separate column in the spreadsheet. The column shall have header by the format <Object name> - <Property name> - <Statistical function>, for the "Number of objects" the format shall be <Object name> - Number of objects

To add another object (and its property(s)) to output - user shall click "+ Output property" button again.

Add formula output property

By click the corresponding button, several fields shall appear, e.g.:

Here, the following controls shall appear:

text input field - to specify the formula using an arbitrary number of properties:
- any character from a to z can be used as the variable
- +, -, *, / and () can be used as the arithmetic operations
- numbers are allowed
near the formula field, there should be the remove button that shall remove the current formula (and its options - variables and name settings)
for each variable from the formula field, there shall be a separate dropdown list (such dropdown list(s) shall appear automatically as new variable(s) was specified in the formula field). Each dropdown shall include a list of available object properties in the format:
```
[<Object name 1>] <Property name 1>
[<Object name 1>] <Property name 2>
[<Object name 2>] <Property name 1>
...
```
text input field - to specify the formula name (that name will be displayed as the header of the corresponding column in the output spreadsheet)

Example of the specified formula:

To add another formula to output - user shall click "+ Output formula" button again.

Object properties

For each object, found via the image analysis, there should be own set of properties. Any object shall have mandatory property Number of objects - total count of the object entities per image. This property can not be combined with the statistic aggregate. All other object properties shall be aggregated with the one/several static aggregates (Mean, Median, StdDev, CV %, Max, Min, Sum)

Properties by objects:

objects, found by the "Find Nuclei"/"Find Cells"/"Find Cytoplasm" method:
- Number of objects
- Area - the area of the object entities in pixel units
additionally for objects, found by the "Find Nuclei"/"Find Cells"/"Find Cytoplasm" and used as parent region for the "Find Spots" method:
- Total Spot Area - the total area of all spots detected in the object entity in pixel units
- Relative Spot Intensity - is defined as the ratio of integrated signal from all pixels of all spots (the signal being intensity within the spot minus the local Spot Background Intensity) and intensity integrated over the object entity
- Number of Spots - number of spots in each object entity
- Number of Spots per Area of <Object name> - is the number of detected spots divided by the area of the object entity
objects, found by the "Find Spots" method:
- Number of objects
- Spot Area - the area of the spot region in pixel units
- Mean Spot Intensity - is the mean intensity of the spot
- Spot Background Intensity - is the mean intensity of the spot border
- Corrected Spot Intensity - is the Mean Spot Intensity minus Spot Background Intensity
- Relative Spot Intensity - is the ratio of the Corrected Spot Intensity and the Mean Spot Intensity
- Uncorrected Spot Peak Intensity - is intensity of the most intense spot pixel
- Spot Contrast - is (A-B)/(A+B) where A is the Uncorrected Spot Peak Intensity and B is the Spot Background Intensity
- Region Intensity - is the mean intensity of the spot search region where the particular spot is located (e.g. cell)
- Spot To Region Intensity - is the Mean Spot Intensity divided by the Region Intensity

Other options

Approach of the analysis task launch and run? (TBD)
All properties values during the analysis shall be calculated per well - no matter how many fields are selected

epam / cloud-pipeline