If you’ve exported spreadsheets to multiple subfolders, you can repeat the import sequence for the contents of each folder. Select, name and then import the remaining sheets to complete the database. That sheet will be added to the database and removed from the list, but the importer will remain open until we’ve finished with all the sheets we’re opening. To do this, uncheck all but one of the input sheets (you can click on it to get a preview in the bottom half of the window), enter a name for the table at the top of the window and hit OK. The settings will largely be automatic if we’re using CSV files, but importantly we need to import the selected sheets individually as separate tables. You should then see the screen below, which will allow you to configure the import. In the resulting popup, navigate to and select all the spreadsheets that we need to import. In the top menu hit “ File - Import - Table from CSV file…” To turn our spreadsheets into tables we need to import them.
Since we’re going to be importing our tables we can just hit “ Cancel” to return to the main screen. Once that’s done you’ll be asked to start defining a table. Select this and provide a destination for your new database (.db) file. If we open DB Browser, we should see a “ New database” button in the top left. This free program provides all the tools we’ll need to turn.
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To create a database, on either Mac or PC we recommend installing DB Browser for SQLite from. For this workflow we’ll be using SQLite databases, since these are easy to work with and don’t require a server. Because of this we can generate a database from a series of spreadsheets. Step 1: Creating a database from output spreadsheetsĪ database file is largely just a series of tables.
properties file with which to load it into CellProfiler Analyst.
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This blog post will cover how to convert a spreadsheet into a database and make a usable. Fortunately, you don’t need to re-run the entire experiment to get your data into CellProfiler Analyst. properties file explaining what to do with that database. We’ve all done this before – CellProfiler Analyst needs a database file, but your CellProfiler pipeline that took days to run was set up to export spreadsheets.
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