Image naming format for uploading


#1

Hi, I have been trying to upload my images for analysis but unsure what I can do. I have tried to follow the instructions for “loading image stacks & movie” but in the metadata section, i have series and frame = 0 while size C, T & Z are all 1.

In my experiment, there are 5 views per well and 5 stacks per view. Ultimately I would like to do a maximum projection of all the stacks first before analysing the 5 different views of the same well. The image naming format by operetta is currently as below

r07c02f01p01-ch1sk1fk1fl1.tiff

r = row, c = column, f = field , p = stack

I am curious if I need to rename the file in certain ways? If not, can anyone point me to the right direction please?

many thanks!
shu


#2

Hello,

Can you please follow a lead in this discussion
I.e. You can preprocess metadata by ImageJ, then save the files with new properties, then reload into CellProfiler.

Let’s see if that would help.


Analyzing the Making Projection Image
#3

In my experiment, there are 5 views per well and 5 stacks per view. Ultimately I would like to do a maximum projection of all the stacks first before analysing the 5 different views of the same well.

You don’t need to rename them, in the Metadata module put the following expression in the ‘Extract from file name’ field to get all the information you need:
r(?P<WellRow>[0-9]{2})c(?P<WellCol>[0-9]{2})f(?P<Site>[0-9]{2})p(?P<Stack>[0-9]{2})-ch(?P<ChannelNumber>[0-9])

However, CP won’t allow you to project a Z stack then do further analysis of that Z stack projection in the same pipeline- you’ll either need to make your Z projections in a separate pipeline (Set the Groups to ‘Well’+‘Site’, then use the MakeProjection and SaveImages modules to create your projections), or do them in another program like Harmony, ImageJ, etc.


#4

Hi Beth,

Thank you very much for your guidance on this! I have used your code for the metadata module and also created a Z stack projection using a separate pipeline. However I am curious if this means I have to individually do a max projection for all individual fields (5 views/well) and same for all other 71 wells I have? Or is there a quicker way?

I have taken some screen shots and wondering if you can have a quick look and guide me to the right direction? I am still new exploring CP and it is a bit overwhelming at times…

Many thanks for your help!

Kind regards
Shu-oi

[cid:image001.png@01D27D47.2DA2CE00]

[cid:image002.png@01D27D47.2DA2CE00]

[cid:image003.png@01D27D47.A842B620]

[cid:image004.png@01D27D47.A842B620]

[cid:image005.png@01D27D47.A842B620]

[cid:image006.png@01D27D47.A842B620]

[cid:image007.png@01D27D48.2A4BE560]


#5

No, you definitely don’t have to do them all individually!

  1. Load up all of your images
  2. Use NamesAndTypes to group by channel only - here you only have one channel, so a single entry with something like Metadata Does Have Channel matching 1. Don’t specify any Well or Site information in NamesAndTypes
  3. Group by Plate (if you have more than one plate), Well, and Site- CP will make and save max projections of each Well+Site individually.

#6

Thanks Beth! It’s all good now!