omero-metadata 0.12.0

Examples

The examples below will use the default automatic column types detection behaviour. It is possible to achieve the same results (or a different desired result) by manually adding a custom # header row at the top of the CSV.

Project / Dataset

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

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

Using Image Name and Dataset Name:

project.csv:

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

The previous example will create an OMERO.table linked to the Project as follows with a new Image column with IDs:

Note: equivalent to adding # header s,s,d,l,s row to the top of the project.csv for manual definition.

Using Image ID and Dataset ID:

project.csv:

image id,Dataset ID,ROI_Area,Channel_Index,Channel_Name
36638,101,0.0469,1,DAPI
36639,101,0.142,2,GFP
36640,101,0.093,3,TRITC
36641,101,0.429,4,Cy5

The previous example will create an OMERO.table linked to the Project as follows with a new Image Name column with Names:

Note: equivalent to adding # header image,dataset,d,l,s row to the top of the project.csv for manual definition.

For both examples above, alternatively, if the target is a Dataset instead of a Project, the Dataset or Dataset Name column is not needed.

Screen / Plate

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:

$ omero metadata populate Screen:1 --file path/to/screen.csv

screen.csv:

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.

Note: equivalent to adding # header well,plate,s,d,l,d row to the top of the screen.csv for manual definition.

ROIs

If the target is an Image or a Dataset, a CSV with ROI-level or Shape-level data can be used to create an OMERO.table (bulk annotation) as a File Annotation linked to the target object. If there is an roi column (header type roi) containing ROI IDs, an Roi Name column will be appended automatically (see example below). If a column of Shape IDs named shape of type l is included, the Shape IDs will be validated (and set to -1 if invalid). Also if an image column of Image IDs is included, an Image Name column will be added. NB: Columns of type shape aren’t yet supported on the OMERO.server:

$ omero metadata populate Image:1 --file path/to/image.csv

image.csv:

Roi,shape,object,probability,area
501,1066,1,0.8,250
502,1067,2,0.9,500
503,1068,3,0.2,25
503,1069,4,0.8,400
503,1070,5,0.5,200

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

Note: equivalent to adding # header roi,l,l,d,l row to the top of the image.csv for manual definition.

Alternatively, if the target is an Image, the ROI 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.

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