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PerkinElmer Informatics Support Forum | ![]() |
Topic Title: Importing Single Cell results from Harmony into Spotfire HCP for use with Image Column Topic Summary: Created On: 2/13/2018 5:14 AM Status Post and Reply |
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- 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
Edited: 2/13/2018 at 5:27 AM by Jace |
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