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Topic Title: Importing Single Cell results from Harmony into Spotfire HCP for use with Image Column
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Created On: 2/13/2018 5:14 AM
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 2/13/2018 5:14 AM
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Joined: 5/9/2014

- In Harmony save the results file to be imported into HCP as “Evaluation Results per well and Object (Tab-separated Text)” (SettingsData 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 AddFile 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)


- 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 DiscoveryInsert 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


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:

Edited: 2/13/2018 at 5:27 AM by Jace

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