Overlay image

Hi there,
I started to play around with the CPAnalyst and I was wondering whether there is any possibility to see the outlines of each object. My objects are not yet cleaned up and do contain a lot of small crap objects but without the outlines it’s hard to decide wether I’m looking at a crap object or not. I wanted to use the CPAnalyst to find a combination of features which enables me to distinguish between crap and ‘real’ object…
I stored the outline-image in CellProfiler with ‘SaveImages’ and checked the ‘Store file and path information…’ but I cannot find a way to load these images in CPAnalyst.


You are on the right track, by first using SaveImages to save the outlines object. Now look in your auto-generated properties file, and there is a section like that below

[code]# ==== Image Path and File Name Columns ====

comments removed…

image_path_cols = Image_PathName_OrigBlue,Image_PathName_OrigGreen,Image_PathName_NucleiOutlines,Image_PathName_CellOutlines
image_file_cols = Image_FileName_OrigBlue,Image_FileName_OrigGreen,Image_FileName_NucleiOutlines,Image_FileName_CellOutlines[/code]

As long as your database includes these PathName and FileName columns, as well as lines defining the default names

image_names = Cherry,GFP,Nuclei,Cells

and colors

image_channel_colors = red,green,gray,gray

you should be all set. (Another setting, “image_url_prepend”, can be used, but unless you have gone to the trouble of setting up a webserver set to redirect your image locations, you can leave this one blank).

These should have been generated automatically if ExportToDatabase was set OK. If not, were you using SQLite or MySQL as your export option? Also, I haven’t checked, but was the CPA manual not helpful for all this info?


Hi David,

thanks a lot for your help. I guess it was a combination of wrong chosen settings in Cellprofiler. First, I thought it would be enough to generate an overlay image but then the ExportToDB-module does not provide these image for export. Then I realized that I have to use the SaveImages-module. But still I could not choose those images for database export.Then, I realized that I have to set the flag to ‘store file and path information’. As the documentation says that this is important for database export, I assumed that these images now automatically would be exported (which is not the case). But today I realized that the images now can be chosen to be exported to the database. Now, everything seems to be fine :smile:

Great, I’m glad you found the “Store file and paths” setting. Thanks for writing back.

Your assumptions were reasonable, and we have thought to set them as default (saving of outline images, and especially saving file and path information). However in high throughput, it gets ‘expensive’ to save images and/or extra columns to the database, so we have gone with an ‘opt in’ approach.