Background

In similar way as we've implemented the support of the "Patology images" previews in the Cloud-Pipeline, we should implement the support of previews of HCS images received by confocal microscopy methods.

Approach

For our issue, each HCS image represents a scope of raw tiff images and metadata xml file(s) united by one measurement.
We shall implement the ability to preview that image bunches as united objects.

Short description of HCS image in context of our issue:

• each measurement includes one or several plates with images
• each plate contains wells. Possible count of wells in a plate is strictly defined. Wells can be with or without images "inside"
• we are interested in wells with images. Inside each such well:
  • there is one or several fields. These fields are similar to puzzle parts (or patches on the patchwork) - all together they consist the well image
  • also, well images can be aggregated by different entities:
    • channels - defined the channels in which raw images were received (e.g. fluorescence)
    • planes - different planes of the scanning depth (different z-coordinates)
    • sequences - images that are made by certain timeseries

Data structure

The minimal intended structure for the raw images data in the object data storage should be the following:

• all data is grouped into measurement folders. Each measurement is represented by one folder, and the name of that folder corresponds to the measurement name
• inside each measurement folder, there are:
  • "Images" folder and inside that folder:
    • tiff raw image files corresponding to that measurement
    • an images info file in xml format ("Index.xml") created during the export of the raw data from the scanner
  • an additional "synthetic" file, created by DTS during the upload raw data to the storage:
    • this file should be tagged by necessary measurement metadata
    • this file shall have the name equals measurement name/ID and .hcs extension (TBD)
    • this file shall be indexed and added to the "Data catalog" search engine (i.e. showing in the Advanced search)
    • exactly for this file, we should add the ability to open preview of the HCS images corresponding to the specific measurement

Open preview

There shall be the following ways to open a preview for the HCS images:

• from the "Attributes" panel of the measurement "synthetic" file - by the corresponding link
• by click the specific icon near the measurement "synthetic" file name in the folder
  
• by click the info icon near the found "synthetic" file via the Advanced search:
  

Preview pop-up

Preview pop-up shall contain:

• measurement file name
• object data storage name where the measurement is stored
• full path to the measurement file
• section of the measurement metadata
• section with the preview

In general case, the preview pop-up should look like the following:

Plate panel

For each HCS measurement, there are one or several plates that include own bunches of images.
Plates are defined inside the <Plates> tag of the index.xml file.
At the Plate section, there should be:

• dropdown list with all plates of the current measurement. By default, the first plate from the list should be loaded. Multiselect is not allowed
• grid with wells. Size of the grid is defined by <PlateRows> (count of rows in this plate) and <PlateColumns> (count of columns in this plate) tags inside the <Plates> tag:
  • full-size wells grid should be shown
  • in the grid, wells that have images should be highlighted separately (blue color on the scheme above):
    • all such wells are described by tags <Well> inside the <Plates> tag
    • position of each well at the grid can be received from each <Well> tag - inside the <Wells> tag
  • in the grid, user can select a desired well - by click it:
    • selected well should be highlighted separately (yellow color on the scheme above)
    • user shall have the ability to select a well only from wells that have images
    • by default, the first well with the tag <Well> from inside the <Plates> tag should be selected
    • multiselect is not allowed

Well panel

This panel should include:

• label with the selected well ID
• the symbolic "map" that demonstrates which part of the image of the selected well is currently shown in the image preview frame on the left side

On the symbolic "map", should be shown:

• available part of the whole selected well - part that is covered by images (blue color on the scheme above)
• separately, the currently "zoomed" part of the whole image (yellow color on the scheme above)
  DETAILS WILL BE CLARIFIED LATER...

Each well includes one or several field. An own raw set of tiff files corresponds to each field.
So, the whole well image consists from all available fields.

Field of the image can be defined by the tag <FieldID> inside the <Image> tag.
Position of the fields on the well image can be defined by tags <PositionX> and <PositionY> inside the <Image> tag.

Channel panel

This panel shall include all channels list corresponds to the current plate.
Total image in the image preview frame should be shown as additive blending of well images of the selected channels.
By default, all channels should be selected.
Full list of channels can be received from inside the <Map> tags - entries with ChannelID option.

For each channel item at the Channel panel, there should be:

• checkbox to enable the channel
• label with the channel name (from <ChannelName> tag inside the <Map> tag)
• control to set the color in which images of that channel should be highlighted
  • TBD about the default color scheme
• control to expand the channel settings:
  • here, the horizontal slider of the channel contrast should be placed

Example of the image above with the disabled violet channel (Ch_1):

Example of the image above with expanded violet channel settings and regulation of the channel contrast by the slider:

Stack panel

This panel shall allow to change the plane of the displayed well image (i.e. to view images on different depth by z-coordinate).
The count of well planes can be defined as max value of the PlaneID values (<PlaneID> tags inside the <Image> tags).
Stack panel should be shown for the plate, only if the count of planes is more than 1.

This panel should contain:

• vertical slider to switch between the planes:
  • by default, the plane with ID equals 1 should be selected
• each tick on the slider should corresponds to certain plane
• each tick should shave the value of z-coordinate (<PositionZ> tags inside the <Image> tags) corresponds to that plane
• label with the unit of the z-coordinate value

Example of the Stack panel for the well with 4 planes:

This panel should be located under Well panel (when the count of planes is more than 1).
Let's suggest that well image from the main scheme above has 3 planes and we've switched to another one. The view should be like:

Time series

Well images can be scanned in different time points. The series of the same well images in different time points are united in sequences.
Note: often, all images are made in a single time point of a single sequence

If there are several sequences for the plate or in any sequence the count of time points is greater than 1, the Time series panel should appear under the image preview.
By this panel, user shall have the ability to select a sequence or/and a time point in a sequence - to receive the well images corresponding this time moment.

The count of sequences can be defined as max value of the SequenceID values (<SequenceID> tags inside the <Image> tags).
The count of time points in a sequences can be defined as max value of the TimepointID values (<TimepointID> tags inside the <Image> tags) for the same SequenceID.

Time series panel should contain:

• a list of expandable sections:
  • each section corresponds to a single sequence
  • label of the section should contain the sequence ID and count of the time points in this sequence
• user shall have the ability to expand the desired sequence section and select the desired time point of the sequence
• by default, the sequence and time points with IDs equal 1 should be selected
• multiselect is not allowed

Example of the Time series panel with 3 sequences: