Sorry for dragging this out for so long, but it’s been quite difficult to make this thing work. (This post has been edited heavily as I figured some things out. Apologies.)
Right now I can open up the Analyst using the properties file generated by the **sqlite **mode, but it does not find the images. Even though the path and filename are correct in the error message, it cannot open the tif files at the image viewer-at least this is the error message. I’m not sure what to do with this. (Just to be on the safe side I coped both the outline images generated by cell profiler to the original directory, and the image files into the output directory.
This is the message:
*An error occurred in the program:
Exception: Could not open image: “C:\0 Powell\cell profiler\2011 12 07 HEK-TR339 2hpi titration on BHK\2011 11 30 HEK-TR 2hpi titrated on BHK 1_1 1_c2.TIF”
Traceback (most recent call last):
File “cpa.py”, line 270, in launch_image_viewer
File “imageviewer.pyc”, line 216, in init
File “imageviewer.pyc”, line 552, in OnOpenImage
File “imagetools.pyc”, line 52, in FetchImage
File “imagereader.pyc”, line 26, in ReadImages
File “imagereader.pyc”, line 81, in read_images_old_way
File “imagereader.pyc”, line 123, in ReadBitmap
File “imagereader.pyc”, line 168, in GetRawData
I think the location of the images might be the problem for the analyst somehow, even though it is looking for them in the right place.
When I use msql/scv then the SQL_1_40_Object.CSV files will not contain headers. (See the files.) None of those files (image/object) contain anything like what the cell profiler analyst manual specifies (chapter IA). I used both the export to spreadsheet and the export to database module, so I have two sets of csv files. The image and cell files generated by the export to spreadsheet module do not contain any information about the images location, but it does have the necessary headers that define what the different columns actually mean.
When I try to open up the Analyst using this properties file generated by this module, however, nothing happens -probably because it is looking for the header information.
I found a really good exercise online how to classify cells using cell profiler and analyst, but the metadata they used was in a csv file to begin with, and both programs used that. I don’t have the metadata prepared this way.
I uploaded the properties files as well. Since the forum did not allow either the .properties extension or .txt, I renamed them .csv.
I really appreciate your help, and I wish you a merry Christmas.
sqlite_DefaultDB_properties.csv (6.45 KB)
mysql_csv_DefaultDB_properties.csv (6.43 KB)
SQL_1_40_Object.CSV (7.93 MB)
SQL_1_40_Image.CSV (45.5 KB)