Could you post the CellProfiler pipeline that generates the CP Analyst example SQL database? I am having problems loading the auto generated SQL setup scripts for my experiment. It seems that loading the image table always gives the “Error 1146 Table ‘sbsdb.per_image’ doesn’t exist” message. Yet a copy of the image measurement CSV file is in the directory along with the object measurement table CSV file. Also, where is the option in CellProfiler to put ‘X’ quotations around fields? I checked the demo mysql experiment database with phpmyadmin and the example script generated all 3 correct tables. However, my custom CP pipeline generated a mysql database setup script that only load the object table CSV file. Also, the image crop feature is broken for my databases but not for the demo. Do I have to save and rename my multichannel TIFF images as single channel PNG files before using the cell phenotype classifier? Thank you for any help with these problems!
If you’re using Windows, perhaps this thread might clear up some of your problems:
Let us know if this doesn’t help and I can look for the CP pipeline.
When cropping in CPAnalyst (you are referring to the last setting in a CPA Properties file “Width of Cropping square”, right?), you might try setting a new crop size, then save the Properties file, quit and re-launch CPA. It had been buggy this way. See this post and thread: viewtopic.php?f=12&t=471#p1611
And yes, you will need to convert your multichannel TIFFs to single channels for CPA to read them properly. They can be single-channel TIFFs, PNGs, etc. We are planning to support multipage TIFFs in CellProfiler and CPAnalyst in the future.
Here’s the original pipeline (to my knowledge at least), attached. The output was changed a bit manually, like the SETUP.SQL filename, etc.
Let me know if this helps or not.
DefaultOUT__1_PIPE_only.mat (2.32 KB)
I am trying to run demo example (CPAExampleDB) but getting error. i am running this in windows.
An error occurred in the program:
AssertionError: PROPERTIES ERROR (image_table): Field is missing or empty.
Traceback (most recent call last):
File “cpa.py”, line 351, in
File “Properties.pyc”, line 80, in show_load_dialog
File “Properties.pyc”, line 156, in LoadFile
File “Properties.pyc”, line 219, in Validate
this is the example.properties file
db_type = mysql
db_host = localhost
db_port = 3306
db_name = CPAnalystExample
db_user = root
spot_tables = per_image
uniqueID = ImageNumber
objectCount = Image_ObjectCount_ObjectCount_Nuclei
cell_tables = per_object
objectID = ObjectNumber
info_table = well_id
info_to_spot = well
geneinfo_table = info_table
geneinfo_col = Hairpin
webinfo_table = info_table
webinfo_col = refseq
webinfo_url_prepend = ncbi.nlm.nih.gov/gquery/gquery.fcgi?term=
image_transfer_protocol = local
image_size_info = N
red_image_path = Image_PathNames_Path_OrigActin
green_image_path = Image_PathNames_Path_OrigpH3
blue_image_path = Image_PathNames_Path_OrigDNA
red_image_col = Image_FileNames_Filename_OrigActin
green_image_col = Image_FileNames_Filename_OrigpH3
blue_image_col = Image_FileNames_Filename_OrigDNA
cell_x_loc = Nuclei_Location_CenterX
cell_y_loc = Nuclei_Location_CenterY
classifier_group_table = well_id
classifier_group_col = well,Hairpin,RefSeq
classifier_per_object_ignore_substr = ImageNumber,ObjectNumber,Location,parent
cell_size = 75
Sorry for the inconvenience, the example you downloaded was not the correct one. See this post: CellProfiler Analyst Example Data FIX