- In Harmony save the results file to be imported into HCP as “Evaluation Results per well and Object (Tab-separated Text)” (Settings … Data Management … Export Data). This will produce an “indexfile.txt” file together with an accompanying Objects Population file containing the results.
- In Spotfire with HCP:
- File menu … Open … “Index File” … OK
- File menu … Add Data tables
o Add … File then select your objects file for instance in this example we will refer to it as “Objects Population Nuclei”
o Select “Tab” delimiter and Refresh
o Ignore the first rows from “Database Name” to “[Data]”
o Set the row containing Row, Column, Plane etc to the “Name row”
o OK
o From “Add Data Tables” view click “Manage Relations…”
o Select to “Show relations for: “indexfile” and click “New”
Left data table : indexfile Right data table : “Objects Population Nuclei”
Left column: Column Right column: Column
(no methods in either table)
OK
- Insert menu … Columns
o In Insert Columns - Select Source
§ Add columns to data table: select “Objects Population Nuclei”
§ Add columns from: From Current Analysis and select “indexfile”
§ Next
o In Insert Columns – Match Columns
§ Match; Row, Column, Plane, Timepoint and Field from current to new data
§ Finish
- Insert … Visualization … In this example set Data table to “Objects Population Nuclei” (this will yield an analysis view to work with, adjust columns as required)
- Insert menu … Transformations …
o Data table: “Objects Population Nuclei”
o Transformation: Pivot
o Add
o In “Pivot Data”dialog:
§ Row identifiers; Row, Column, Plane, Timepoint, Field, Object No
§ Column titles (%C): Channel Name
§ Values (%V) and aggregation methods (%M): URL
§ Column naming pattern: (%V) for %C ( This uses the Values with Column title in the naming separated by “for” )
§ In Tranfer columns (%T) and aggregartion methods (%A).
· Click on the down arrow to the right of None in this field and “Select Columns”
· In Available columns field, select all or a subset of columns and click “Add>”
· In “Selected columns” field select all columns and change Aggregation to “First” check that all are listed as “First” then click OK
§ Transfer column naming pattern: %T ( %T this will set the name of the columns from the Transfer columns)
§ Check the “Sample” view at the bottom of the dialog, if it looks good click OK.
- At this point you should see a URL per channel for each object line in the table
- Tools menu … Image Discovery … Insert Image Column
- Choose a rule type to be used from the dropdown for Harmony Data:
o Harmony URL Cell Image Rule – Rule supports rendering of cropped cell images in TIFF format with cell level result files from Harmony
OR
o Harmony URL Field Image Rule – Rule supports rendering of field images in TIFF format with result files from Harmony
- Choose the “Value” for the URL, this will be one of the three channels i.e “URL for BOBO-3”
- Click OK, check the rendering then add other Image Columns as required i.e 1 per channel
More info on Pivots Data in Spotfire here:
https://docs.tibco.com/pub/spotfire/7.0.1/doc/html/data/data_details_on_pivot_data.htm