MakeProjection CellProfiler Module - Can only load a single image?

Hi all,

I am trying to use the MakeProjection module in CellProfiler to create a composite image of several different channels from the same field of view.

As an example I have two subfolders loaded into the Images module, each containing three files of the format:


I have then clicked Yes to ‘Extract metadata’ and ‘Extract from file/folder names’; used the Metadata source as ‘Folder name’ and the regular expression .*\/$ to generate metadata for the six images.

I have used NamesAndTypes with Images Matching Rules to assign each of the images with DNA in the name as named DNA, CD3 as CD3, etc. I have selected the intensity range from ‘Image bit-depth’.

I have then used Groups and selected FileLocation as my Metadata category. This gives one entry in the ‘Grouping list’ section with a count of 2 and two Image Sets each made up of three files in the field below.

My problem comes when I then want to make a single image which is a projection of all three of the images in an Image Set. i.e. I want to produce a single composite image made up of DNA, CD3, and Pan-Keratin, for each of my two image sets.

When I use the MakeProjection module, the ‘Select the input image’ command only allows me to select one of my three images (DNA, CD3, Pan-Keratin) from which to make a projection and not more than one.

How am I able to select all three channels to produce a composite image?

Do I need to alter my grouping somehow so that a whole group of images appears as an object to make into a projection?

Thanks in advance,