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Topic Title: Columbus - Extract at Scale Cell Level Data from "Population Table"
Topic Summary: How can I extract the Population table from every well of every plate at scale? There are too many plates, wells and fie
Created On: 5/14/2019 8:02 PM
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 5/14/2019 8:02 PM
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trentbrick

Posts: 1
Joined: 5/14/2019

Hello. I want to be able to extract from Columbus all of the features I have made from the Image Analysis *and* the XYZ coordinates of each specific cell in each well for every plate being analyzed. I have found that under Image Analysis if I apply my Building Blocks I get a table that has all of this data for me (this Table is separate from the Results table). However, this Population data is lost when I use this Image Analysis Acapella Script for Batch Analysis and then Secondary Analysis.

How can I extract the Population table from every well of every plate at scale? There are too many plates, wells and fields within each well to download every single one of these by hand (clicking the "Download" button). I'd rather not have to use the command line but I am proficient in using it and it seems like there may be some way to connect to the server backend? How could I do this and then apply some sort of Batch Analysis to every plate and well that would output the Population table rather than the Results table? If there are specific functions I can place at the end of my Acapella Script that is generated from the Image Analysis step that would be one way for me to do it? Just an idea but I am happy to do something else too if it will work.

Thank you for any help that can be provided.

Trenton

 5/17/2019 5:03 AM
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NW

Posts: 57
Joined: 5/13/2014

Hi Trenton,

Following batch analysis, and as long as you have defined object level results in your analysis script, you can export the results files via the Export view in Columbus and the exported files should give you all the object level parameters.

Best,

Nick

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