CellProfiler - Can you name all images in a set at once (in one step) in NamesAndTypes using values in a Metadata column?

cellprofiler

#1

Dear community,

Working in CellProfiler -

If you have an image set and would like to name each image in this set (in NamesAndTypes) using a value assigned to it in a Metadata column from the Metadata module, is there a way to do this for all images in one go rather than manually naming images in your set one by one using ‘Images matching rules’ -> ‘Metadata does Exactly Match …’?

For example, suppose each image in your set has a Metadata value for ‘Antibody’ assigned to it, contained in an ‘Antibody’ column in the Metadata module.

Is there a method to implement ‘Assign to all images’ … ‘Name to Assign these images’ does exactly match ‘Metadata > Antibody name’ so that all images are assigned a name matching the Antibody value in one go without assigning names to images one by one?

Many thanks
Emma


#2

Hi Emma,

I’m pretty sure the answer is no… also I’m finding it hard to imagine why you might need to do that? Could you maybe explain why as there might be another way to achieve it.


#3

Hi,

Interested in doing this to save time/reduce human error in assigning names manually one by one if we are just needing to pull names from a single metadata column.

Rather than ‘Add another image’ one by one in the NamesAndTypes module it would be helpful to just be able to use a single command to assign an image’s name to its value in a chosen Metadata column.

Hope that makes sense.
Thanks for your help!


#4

Okay, I’ve listed a few useful things you can do with Metadata tags below that I’m hoping help somehow.

For anything where you are naming images or folders you can right click in the text window and you will get a dropdown menu that says “Insert tag” and then has a list of your metadata tags.

So for saving images for example, in your scenario if you had Image1_{Antibody} then each image saved will be named with whatever Antibody name is in it’s metadata tag.


This also works for folder paths. In this case the result will be separate directories with the images belonging to each metadata tag being in their respective folders.

image

Finally, just in case you missed it in ExportToSpreadsheet you can tick “Add image metadata columns to your object data file”.

Could either of these features help you?

Good luck,
Laura


#5

Thanks for sharing.

Unfortunately I don’t think any of these apply to our situation where we’re looking to name images by metadata tag in the NamesAndTypes module itself rather than in any downstream SaveImages modules.

We were hoping there might be an option to Assign names to all your images in one go equal to their metadata tag (in the NamesAndTypes module).

Thanks for all your suggestions though. Greatly appreciated.


#6

Okay Emma, sorry for not being helpful.

Do you want to do this because you need to run different modules on different groups of images?


#7

Hi,

No- thank you for your help! It’s greatly appreciated. I may not be explaining my question clearly.

We’re doing this as we don’t want to sequentially run each image through the pipeline as its own image set but can instead read all images into the one pipeline together. Some images may require different modules to others hence not passing them through sequentially.

Hope that makes sense!


#8

Oh, it’s no problem. I think I was just having trouble visualising the whole problem not knowing the whole project but I think I get it now.

So, what it comes down to is that, ideally, you would be assigning multiple names using separate rules to the same images and I’m pretty sure CellProfiler can’t deal with that.

It could be there’s something else I’m missing that someone more in the know will turn up and let us know about it. :crossed_fingers: