Information Table

cellprofiler-analyst

#1

in the properties file, one can upload an information table, which, apparently, can link image numbers to gene names.

could you please provide an example how such a table should look like?!

is it just a text file with

1,geneA
2,geneB

or some other format?

thanks,
Christian.


#2

Hi Christian,

Yes, this is the most basic format. You simply need a table with linker column that is shared by the image table and your metadata table (e.g., IMAGE NUMBER) plus another column of gene names. Also, as the manual says, you can also have other information in this metadata table like a Web Information Column that will allow you to easily link to external web-accessible databases.

David


#3

thanks!

sorry but I don’t understand completely:

(i) what is the ‘image table’ and what is the ‘metadata table’ ?

(ii) do I have to write something above the columns to specify that this is ‘IMAGE NUMBER’, or does the software automatically assume that this is the first column?

(iii) are the columns really ‘,’ separated, as in my example, or rather ‘tab’-separated, or something else?

cheers,
Christian.


#4

CPAnalyst interacts with MySQL databases (and possibly Oracle databases, although we’re not fully supporting that now). So you need to get information into a database first. If you need help with setting up a database, you’ll need to contact your local IT staff.

(i) CellProfiler’s ExportToDatabase module generates “Per_Image” and Per_Object" tables by default. They hold information, including measurements, about images and objects respectively, and are uploaded to your MySQL database via the *SETUP.SQL script that is also generated by ExportToDatabase. See the Help for ExportToDatabase for details. You may also upload (however you choose) what I call “metadata”, usually in another table or as columns added to your Per_image table, which holds information about the experiment, e.g. gene names for RNAi, or treatment/drug information for an individual image or well ID for chemical screens, etc.

(ii) See the generated *SETUP.SQL script for examples on how to create tables within databases. So no, you do not need to write something “above” columns - that sort of header information is constructed by MySQL commands (e.g. “CREATE TABLE”). See MySQL online help for extensive documentation. There are many free tools that will help you upload this info (e.g. Sequel Pro for Macs) without needing too much database manipulation experience.
ImageNumber must be specified exactly the same in the Per_Image and metadata tables for it to be linked. It does not assume anything by position.

(ii) Once the info is in the database, they are not comma or tab-delimited. Prior to that, you can make the metadata table any way you like (comma, tab or otherwise delimited), so long as you can upload it to the database properly. E.g. Sequel Pro includes tools to upload CSV files, so I have scripts that generate CSV files that include the metadata that I want, then I upload them via File->Import->CSV file or via command line mysql. It simply needs to have a column that has the same column name as in the Per_image table to act as a linker column.

Hope this helps!
David


#5

Dear David,

that helps indeed.

thanks, Christian.