Help & Documentation

Retrieve images

The experimental data set contains images from experiments conducted for the Europhenome project and for the International Mouse Phenotype Consortium (IMPC) project. A record in this resource represents a single data point for an experiment. The list of experiments performed is documented in the International Mouse Phenotyping Resource of Standardised Screens (IMPReSS). Individual data points are associated to an IMPReSS Parameter. Parameters are organised into Procedures. Procedures are organised into Pipelines.

There are many ways to select and filter image records, e.g.:

  • all images for a parameter
  • all images for a gene for one experiment
  • all images for a specific pipeline

The IMPC images data REST API provides the fields described in the table below, which are mostly the same as for the experiment API with some additions. Each field may be used to restrict the set of IMPC image data you wish to receive.

The full SOLR select syntax is available for use in querying the REST API.
See the Solr Wiki, Solr Query Syntax and Common Query Parameters, for a more complete list of query options.

Image specific parameters

Field nameDatatypeDescription

omero_id

int

the omero image id, which uniquely signifies the image in the omero image system

download_url

string

Url from where the original image can be downloaded – the format can be one of many including dicom, tiff, jpeg

jpeg_url

string

Url where a high resolution jpeg of the image can be obtained

General experimental parameters

Field nameDatatypeDescription

phenotyping_center

string

the name of the organisation that performed the experiment

gene_accession_id

string

the gene MGI ID of the mutant specimen used for the experiment

gene_symbol

string

the gene symbol of the mutant specimen used for the experiment

allele_accession_id

string

the allele MGI ID of the mutant specimen used for the experiment

allele_symbol

string

the allele symbol of the mutant specimen used for the experiment

zygosity

string

indicating the zygosity of the specimen

sex

string

indicating the sex of the specimen

biological_sample_group

string

indicating if the specimen was a member of the control group or the experimental group (also see metadata_group)

metadata_group

string

a string indicating a group of experimental and control mice that have the same metadata (see also biological_sample_group)

metadata

list of strings

list showing all relevant metadata in effect when the data was collected

strain_name

string

Deprecated. Please see genetic_background description

strain_accession_id

string

Background strain MGI accession ID (or IMPC ID when MGI accession is not available)

genetic_background

string

indicating the background strain name of the specimen

pipeline_name

string

indicating the name of the pipeline where the experiment was conducted

pipeline_stable_id

string

indicating the IMPReSS ID of the pipeline

procedure_stable_id

string

indicating the IMPReSS ID of the procedure

procedure_name

string

indicating the full name of the procedure

parameter_stable_id

string

indicating the IMPReSS ID of the parameter

parameter_name

string

indicating the full name of the parameter

experiment_source_id

string

indicating the experiment identifier at the center that performed it

observation_type

string

indicating the type of parameter (categorical, unidimensional, multidimensional, time series, metadata)

colony_id

string

indicating the name of the colony of the specimen

date_of_birth

date

indicating the date the specimen was born

date_of_experiment

date

indicating the date the data was collected

weight

float

indicating the weight of the specimen observed

weight_parameter_stable_id

string

indicating the particular weight parameter

weight_date

date

indicating the actual date the weight was observed

weight_days_old

int

indicating the age in days of the specimen when the weight was observed

data_point

float

indicates the measured data value [1][2][3]

order_index

int

indicating the order [2]

dimension

string

indicating the dimension [2]

time_point

string

indicating the time the data value was measured [3]

discrete_point

float

indicating the discrete point [3]

category

string

indicating the category to which the specimen has been classified [4]

value

string

the value of the metadata [5]

[1] – For unidimensional parameters [2] – For multidimensional parameters [3] – For time series parameters [4] – For categorical parameters [5] – For metadata parameters

Examples

NOTE: Certain characters, most notably spaces and the “<” and “>” characters, must be url encoded (space = %20, < = %3c, > = %3e) for command line usage.

Retrieve the first 10 image results for parameter IMPC_XRY_034_001 “XRay Images Dorso Ventral”, for colony MEAW

curl 'https://www.ebi.ac.uk/mi/impc/solr/impc_images/select?q=parameter_stable_id:IMPC_XRY_034_001%20AND%20colony_id:MEAW&wt=json&indent=true'

Retrieve the first 1000 image results for parameter IMPC_XRY_034_001 “XRay Images Dorso Ventral”, for colony MEAW (same as above, except append &rows=1000)

curl 'https://www.ebi.ac.uk/mi/impc/solr/impc_images/select?q=parameter_stable_id:IMPC_XRY_034_001%20AND%20colony_id:MEAW&wt=json&indent=true&rows=1000'

Retrieve impc image results for organisation WTSI

curl 'https://www.ebi.ac.uk/mi/impc/solr/impc_images/select?q=phenotyping_center:WTSI&wt=json&indent=true'

Retrieve impc image results for MRC Harwell for procedure name Echo

curl 'https://www.ebi.ac.uk/mi/impc/solr/impc_images/select?q=phenotyping_center:%22MRC%20Harwell%22%20AND%20procedure_name:%20Echo%20&wt=json&indent=true'

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