Open phicks22 opened 1 year ago
@phicks22 thanks for raising the question with specific examples. Looking at the associated imaging data:
HCS data can either be dense or sparse and the grid
attribute of the webgateway/plate
endpoint exposes imaging data acquired at a given (row,column)
coordinate on a plate layout. Thus the null
values are expected as they reflect the sparseness of the original acquisition.
Hi @sbesson,
I appreciate the quick response.
I see, it makes sense why it would be structured that way. I wouldn't have thought of that.
Thanks! Parker
Hello,
Thanks for making this repo and data public. I’m working with the IDR API (https://idr.openmicroscopy.org/about/api.html) to pull image metadata, but I’m running into an issue.
Specifically, in the JSON API output, the
grid
object indices appear to be inconsistent in some studies. Wheregrid
was obtained by using the following code:Many of the metadata for plate JSON files begin at
grid[0]
, however for plate 1753 (https://idr.openmicroscopy.org/webgateway/plate/1753) the metadata begin atgrid[1]
. See screenshot below:Similarly, if the metadata are located in
grid[0]
, sometimes the metadata won't appear untilgrid[0][1]
instead ofgrid[0][0]
. For example, see specifically https://idr.openmicroscopy.org/webgateway/plate/1760. See screenshot below:Are plate metadata supposed to begin at
grid[0][0]
?This is a potential issue that I can manage, but I’d like to report these observations in case these inconsistencies are errors and can be relatively easily standardized.
Thanks, Parker