Error message when assigning names and types

I am trying to run an analysis pipeline on a set of images that I have, however an error keeps appearing saying that the “names and types” section cannot find any image sets. I have exported metadata from my images including the channel number and used the channel number to give names to my images. The error comes up that image sets 494-792 are missing image “GFAP” (channel 3), however all of my image sets are complete. I have a total of 1512 images, which should make 378 image sets (4 images per set). At the moment it seems to be considering the images individually.

An example of my image names are as follows:

r02c03f01p21-ch1sk1fk1fl1
r02c03f01p21-ch2sk1fk1fl1
r02c03f01p21-ch3sk1fk1fl1
r02c03f01p21-ch4sk1fk1fl1

The regular expression that I am using is:
^r(?P[0-9][0-9])c(?P[0-9][0-9])f(?P[0-9][0-9])p(?P[0-9][0-9])-ch(?P[0-9])

I have attached the project (without images).

If anyone can provide any help, it would be greatly appreciated.

Thanks!20161129 GFAP autophagy pipeline empty.cpproj (93.2 KB)

My guess is that it’s because instead of ‘Metadata does have Channel matching 4’ for your LAMP channel (like you do for your other 3 channels), you just have ‘File does contain 4’, which means any file that has a 4 anywhere in its name is getting mis-assigned. I think if you fix that you should be all set.

Thanks for your suggestion, I just tried that and it doesn’t make any difference. I also tried removing all of the metadata part and just sorting by “file does contain ch1” etc and it still doesn’t work. I also tried including more of the redundant file name and that also doesn’t help.

Can you turn off your ‘Groups’ module? You’ve got it turned on with a grouping of ‘none’, which can cause issues.

Okay, I tried that now, but it made no difference. Under the “names and types” tab, when I click “update” to try and get the list of image sets, it still comes up with a dialogue box saying that the way my pipeline is configured, no image sets can be identified.

Thanks for your help bcimini. I managed to solve the problem, I needed to include .tif at the end of my image criteria in “names and types” for some reason. There also appears to have been a bug in the version that I saved, as when I started again and rewrote the pipeline from scratch this fix worked, but when I tried to input it into the already written pipeline it did not.

1 Like