Custom Plate-type

Hi there,
I’d like to use 48-well plates in both CP and CPA, but I might as well e.g. need a 14x34 plate in the future. I was wondering wether there is an easy way to create such a custom ‘plate_type’ next to the currently supported 96, 384 and 5600 types?

Thanks, Tom

Hi Tom,

Unfortunately there is no such feature at this point but we are planning for a release by the end of October and this might be a relatively easy addition to make. I’ll do my best to get it in, but can’t make any promises unfortunately since I will soon be leaving the group and have a lot to do in a short period of time.

If you have any python coding experience and are running from source then I’d certainly be willing to help you implement it for yourself.

Best,
Adam

Hi Adam,

Thanks for the quick response and clear answer. I’m new to Python, but perhaps if you can indicate the files I need to modify I can give it a try, since as you said it should be relatively easy and examples of 96, 384 and 5600 are present.

Best, Tom

Oof, ok this is ugly… an easy fix, but there’s a lot of crufty code.

properties.py:
supported_values = ‘96’, ‘384’, ‘1536’, ‘5600’]

datamodel.py
add to the plate formats at the top of the file
then edit populate_plate_maps

plateviewer.py
add to the plate formats at the top of the file
edit AddPlateMap

Are you already running from source?

OK, I’ve committed changes myself to clean this code up and allow users to do

plate_shape = rows, columns

alternately, you can still use the plate_type variable and it now supports:
6, 24, 96, 385, 1536, and 5600

Just svn up to the bleeding edge. Relevant files are the last ones I listed and platemappanel.py

-Adam

Hi Adam,

Thanks a lot for supplying all the info and the update in such a short notice, I’ll dig into the updates immediately.

Best, Tom

hi,

just downloaded version 11599 from svn.broadinstitute.org/CellProf … CPAnalyst/

and the plate_shape seems not to be implemented yet…

do i miss something?

cheers, tischi

Right, this is currently sitting in our subversion trunk and hasn’t been included in a release yet.

I probably should have mentioned thought that I could send a bleeding edge build if you or Tom would like one.

Adam,
But it should be in SVN version 11599, right? They are using the SVN version. All the user needs to do is put

plate_shape = <rows>, <columns>
into their properties file?

-David

Ah, my mistake, the link should have been obvious. I found the problem and just committed a fix. Let me know how it works for you.

-Adam

PS: Thanks for catching that, David.

which version do i have to use?

could you please post the address that i should “svn co” ?

thanks :smile:

I’m at svn revision 11600

It looks like you had the right address before:
vc.broadinstitute.org/CellProfi … /CPAnalyst

For a 96 well plate, you could use:

instead of

either should work (but not both at the same time since they might contradict).

works :smile:
thanks!!!