Error encountered while opening DefaultDB

I was not able to open the DefaultDB file in CellProfiler Analyst. I would like to use Plate Viewer in CellProfiler Analyst to look at my results.

Thank you

Please find attached:
Pipeline
Sample images
Metadata
Error messages




Translocation_files_and_wells.csv (2.37 KB)




ArrayScan10X.cp (8.33 KB)

Hi,
Could you also post your properties file?

Not sure of the issue, but to use the Plate Map feature, you need to have these settings in your properties file:
plate_id = <plate_name_column>
well_id = <well_name_column>
plate_type = <96,384, …>

Thanks,
David

Hi David,
Do you mean the DefaultDB? If so, I tried, but it would allow me to. Hence, I need some guidance.
Thanks!
Anna

Hi Anna,

I mean the DefaultDB.properties file. Note that your computer may be hiding the extension (".properties") so it may look only like “DefaultDB”, but it should open in any text editor beginning with something like this:
#Fri May 10 12:31:21 2013

==============================================

CellProfiler Analyst 2.0 properties file

==============================================

If you mean that the Forum won’t allow you to upload a “*.properties” file, then you can rename it to DefaultDB.txt and/or zip the file and I think it should upload.
David

#Mon May 6 16:02:14 2013

==============================================

CellProfiler Analyst 2.0 properties file

==============================================

==== Database Info ====

db_type = sqlite
db_sqlite_file = C:\CellProfiler\Data\04-25-13\images\DefaultDB.db

==== Database Tables ====

image_table = Per_Image
object_table = Per_Object

==== Database Columns ====

Specify the database column names that contain unique IDs for images and

objects (and optionally tables).

table_id (OPTIONAL): This field lets Classifier handle multiple tables if

you merge them into one and add a table_number column as a foreign

key to your per-image and per-object tables.

image_id: must be a foreign key column between your per-image and per-object

tables

object_id: the object key column from your per-object table

image_id = ImageNumber
object_id = ObjectNumber
plate_id = Image_Metadata_Plate
well_id = Image_Metadata_Well

Also specify the column names that contain X and Y coordinates for each

object within an image.

cell_x_loc = Experiment_Location_Center_X
cell_y_loc = Experiment_Location_Center_Y

==== Image Path and File Name Columns ====

Classifier needs to know where to find the images from your experiment.

Specify the column names from your per-image table that contain the image

paths and file names here.

Individual image files are expected to be monochromatic and represent a single

channel. However, any number of images may be combined by adding a new channel

path and filename column to the per-image table of your database and then

adding those column names here.

NOTE: These lists must have equal length!

image_path_cols = Image_PathName_DNA,Image_PathName_protein
image_file_cols = Image_FileName_DNA,Image_FileName_protein

CPA will now read image thumbnails directly from the database, if chosen in ExportToDatabase.

image_thumbnail_cols = Image_Thumbnail_DNA,Image_Thumbnail_protein

Give short names for each of the channels (respectively)…

image_names = DNA,protein

Specify a default color for each of the channels (respectively)

Valid colors are: [red, green, blue, magenta, cyan, yellow, gray, none]

image_channel_colors = red, green

==== Image Accesss Info ====

image_url_prepend =

==== Dynamic Groups ====

Here you can define groupings to choose from when classifier scores your experiment. (eg: per-well)

This is OPTIONAL, you may leave "groups = ".

FORMAT:

group_XXX = MySQL select statement that returns image-keys and group-keys. This will be associated with the group name “XXX” from above.

EXAMPLE GROUPS:

groups = Well, Gene, Well+Gene,

group_SQL_Well = SELECT Per_Image_Table.TableNumber, Per_Image_Table.ImageNumber, Per_Image_Table.well FROM Per_Image_Table

group_SQL_Gene = SELECT Per_Image_Table.TableNumber, Per_Image_Table.ImageNumber, Well_ID_Table.gene FROM Per_Image_Table, Well_ID_Table WHERE Per_Image_Table.well=Well_ID_Table.well

group_SQL_Well+Gene = SELECT Per_Image_Table.TableNumber, Per_Image_Table.ImageNumber, Well_ID_Table.well, Well_ID_Table.gene FROM Per_Image_Table, Well_ID_Table WHERE Per_Image_Table.well=Well_ID_Table.well

==== Image Filters ====

Here you can define image filters to let you select objects from a subset of your experiment when training the classifier.

This is OPTIONAL, you may leave "filters = ".

FORMAT:

filter_SQL_XXX = MySQL select statement that returns image keys you wish to filter out. This will be associated with the filter name “XXX” from above.

EXAMPLE FILTERS:

filters = EMPTY, CDKs,

filter_SQL_EMPTY = SELECT TableNumber, ImageNumber FROM CPA_per_image, Well_ID_Table WHERE CPA_per_image.well=Well_ID_Table.well AND Well_ID_Table.Gene=“EMPTY”

filter_SQL_CDKs = SELECT TableNumber, ImageNumber FROM CPA_per_image, Well_ID_Table WHERE CPA_per_image.well=Well_ID_Table.well AND Well_ID_Table.Gene REGEXP ‘CDK.*’

==== Meta data ====

What are your objects called?

FORMAT:

object_name = singular object name, plural object name,

object_name = cell, cells,

What size plates were used? 96, 384 or 5600? This is for use in the PlateViewer. Leave blank if none

plate_type = 96

==== Excluded Columns ====

OPTIONAL

Classifier uses columns in your per_object table to find rules. It will

automatically ignore ID columns defined in table_id, image_id, and object_id

as well as any columns that contain non-numeric data.

Here you may list other columns in your per_object table that you wish the

classifier to ignore when finding rules.

You may also use regular expressions here to match more general column names.

Example: classifier_ignore_columns = WellID, Meta_., ._Position

This will ignore any column named “WellID”, any columns that start with

“Meta_”, and any columns that end in “_Position”.

A more restrictive example:

classifier_ignore_columns = ImageNumber, ObjectNumber, .Parent., .Children., .Location_Center.,.Metadata.

classifier_ignore_columns = table_number_key_column, image_number_key_column, object_number_key_column

==== Other ====

Specify the approximate diameter of your objects in pixels here.

image_tile_size = 50

======== Auto Load Training Set ========

OPTIONAL

You may enter the full path to a training set that you would like Classifier

to automatically load when started.

training_set =

======== Area Based Scoring ========

OPTIONAL

You may specify a column in your per-object table which will be summed and

reported in place of object-counts when scoring. The typical use for this

is to report the areas of objects on a per-image or per-group basis.

area_scoring_column =

======== Output Per-Object Classes ========

OPTIONAL

Here you can specify a MySQL table in your Database where you would like

Classifier to write out class information for each object in the

object_table

class_table =

======== Check Tables ========

OPTIONAL

[yes/no] You can ask classifier to check your tables for anomalies such

as orphaned objects or missing column indices. Default is on.

This check is run when Classifier starts and may take up to a minute if

your object_table is extremely large.

check_tables = yes

Hi David,
I just copied and pasted the DefaultDB properties since the Forum doesn’t allow .properties nor .txt files to be uploaded.
Thanks again!
Anna

Thanks for posting that. It turns out to be something else, a fairly obscure bug, which Mark details here: viewtopic.php?f=14&t=1605#p6432

Basically, ClassifyObjects doesn’t work well with how SQLite stores information. Try his workarounds and re-run CellProfiler and see if CPAnalyst works for you then.
David

Thanks David. I will give the Cell/particle counting pipeline a try.
Anna