Platevier can not open


#1

Hi

I am a new cellprofiler user, and I am very interesting in the solfware. Recently, I have a lot of image for analytic cell translocation assay. After I get a set of information from CellProfiler, and I want to open my properties date by cellprofiler analyst. I can not open my image when I select plateviewer and the solfware print a message box as following this description. Dose anyone help me to solve the problem ? Any help and guidance will be very much appreciated. Thank you.

An error occurred in the program:
ValueError: max() arg is an empty sequence

Traceback (most recent call last):
File “cpa.py”, line 266, in launch_plate_map_browser
File “plateviewer.pyc”, line 171, in init
File “plateviewer.pyc”, line 368, in OnSelectMeasurement
File “plateviewer.pyc”, line 271, in UpdatePlateMaps
File “plateviewer.pyc”, line 687, in FormatPlateMapData

Hi, there

Again , I have some problem about the plate viewer and I post error message and properties file. I have been edit plate ID, well ID and plate type, but still not work. does anyone know how to edit the properities? Please let me know how to edit my properties, thank you.

Vincent

An error occurred in the program:
ValueError: max() arg is an empty sequence

Traceback (most recent call last):
File “cpa.py”, line 266, in launch_plate_map_browser
File “plateviewer.pyc”, line 171, in init
File “plateviewer.pyc”, line 368, in OnSelectMeasurement
File “plateviewer.pyc”, line 271, in UpdatePlateMaps
File “plateviewer.pyc”, line 687, in FormatPlateMapData

#Mon Sep 14 16:43:24 2015

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

CellProfiler Analyst 2.0 properties file

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

==== Database Info ====

db_type = sqlite
db_sqlite_file = E:\Image date\BMP4_date_test\20150911_BMP4_new protocol_test\HTS-Screen01-20150911\COS-7\20150914\20150914.db

==== Database Tables ====

image_table = HCS_Per_Image
object_table = HCS_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 = Nuclei_Location_Center_X
cell_y_loc = Nuclei_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_DAPI,Image_PathName_GFP
image_file_cols = Image_FileName_DAPI,Image_FileName_GFP

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

image_thumbnail_cols =

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

image_names = DAPI,GFP

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

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

image_channel_colors =

==== 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.

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


#2

I have the same problem. Anybody have any tips or advice? Thanks!


#3

Hi,

Do you have these 3 fields filled in within your properties file?
plate_type
plate_ID
well_id

Please post your properties file if you are still having trouble.
David