File header sizeC and sizeZ always 1


#1

Dear all,
Happy New Year!
I’m trying to upload MicroManager stacks to CP 2.2.0.Test_header.cpproj (71.8 KB)

Stacks have 2 channels, 1 timepoint and 2 to 5 slices.
The File header section in the Metadata module reads all stacks c=1, z=1 and t=c*z (4 to 10). While it’s not important in this case whether the dimensions are properly recognised as channel, timepoint or slice, it is however important that one of them holds the number of channels and another the number of slices.
I guess the tif header used is not properly recognised. Is there any way I can set the proper dimensions?
I’m uploading an example project and a problem image (2 channels and 2 slices)
Thanks very much for your help
Best regards
Carlos


Failure to load OME-TIFF sample data
#2

Hi Carlos,
Your image didn’t come through. Can you try reuploading? Thanks.


#3

Hi Beth,
I’m sorry, you’re right.
Here it is (zipped): MMStack.zip (8.4 MB)
It has 2 channels, 1 timepoint and 3 slices.
Thanks very much
Best
Carlos


#4

Hi Carlos,

As I explained here Failure to load OME-TIFF sample data
You may try :
First open your image in ImageJ, choose “Image” > “Properties” > make sure it is set with Channel © = 2, slices (z) = 3

Even though you may see it is already set so, please save the image as new anyway (as .tif)

Then load the newly saved image. Open it in CellProfiler.
In Module “Metadata” > “Extract metadata” from “Image file headers” > Update the field.
Now you would see the channel and slices are shown correctly.


Note: Python indexing starts from 0

For multiple images, you can do batch process in ImageJ (basically: open and re-save as new files with correct properties).

Hope that helps.


Image naming format for uploading