omero-metadata 0.8.1

populate

This command creates an OMERO.table (bulk annotation) from a CSV file and links the table as a File Annotation to a parent container such as Screen, Plate, Project or Dataset. It also attempts to convert Image or Well names from the CSV into Image or Well IDs in the OMERO.table.

The CSV file must be provided as local file with --file path/to/file.csv.

If you wish to ensure that number columns are created for numerical data, this will allow you to make numerical queries on the table. Column Types are:

• d: DoubleColumn, for floating point numbers

• l: LongColumn, for integer numbers

• s: StringColumn, for text

• b: BoolColumn, for true/false

• plate, well, image, dataset, roi to specify objects

These can be specified in the first row of a CSV with a # header tag (see examples below). The # header row is optional. Default column type is String.

NB: Column names should not contain spaces if you want to be able to query by these columns.

Examples:

To add a table to a Project, the CSV file needs to specify Dataset Name and Image Name:

$ omero metadata populate Project:1 --file path/to/project.csv

project.csv:

# header s,s,d,l,s
Image Name,Dataset Name,ROI_Area,Channel_Index,Channel_Name
img-01.png,dataset01,0.0469,1,DAPI
img-02.png,dataset01,0.142,2,GFP
img-03.png,dataset01,0.093,3,TRITC
img-04.png,dataset01,0.429,4,Cy5

This will create an OMERO.table linked to the Project like this:

If the target is a Dataset instead of a Project, the Dataset Name column is not needed.

To add a table to a Screen, the CSV file needs to specify Plate name and Well. If a # header is specified, column types must be well and plate.

screen.csv:

# header well,plate,s,d,l,d
Well,Plate,Drug,Concentration,Cell_Count,Percent_Mitotic
A1,plate01,DMSO,10.1,10,25.4
A2,plate01,DMSO,0.1,1000,2.54
A3,plate01,DMSO,5.5,550,4
B1,plate01,DrugX,12.3,50,44.43

This will create an OMERO.table linked to the Screen, with the Well Name and Plate Name columns added and the Well and Plate columns used for IDs:

If the target is a Plate instead of a Screen, the Plate column is not needed.

If the target is an Image, a csv with ROI-level and object-level data can be used to create an OMERO.table (bulk annotation) as a File Annotation on an Image. The ROI identifying column can be an roi type column containing ROI ID, and Roi Name column will be appended automatically (see example below). Alternatively, the input column can be Roi Name (with type s), and an roi type column will be appended containing ROI IDs. In this case, it is required that ROIs on the Image in OMERO have the Name attribute set.

image.csv:

# header roi,l,d,l
Roi,object,probability,area
501,1,0.8,250
502,1,0.9,500
503,1,0.2,25
503,2,0.8,400
503,3,0.5,200

This will create an OMERO.table linked to the Image like this:

Note that the ROI-level OMERO.table is not visible in the OMERO.web UI right-hand panel, but can be visualized by clicking the “eye” on the bulk annotation attachment on the Image.

License

This project, similar to many Open Microscopy Environment (OME) projects, is licensed under the terms of the GNU General Public License (GPL) v2 or later.

Copyright

2018-2020, The Open Microscopy Environment