Open nataliaorlova opened 1 year ago
Here is the first file example generated by LIMS:
"\allen\programs\mindscope\production\vipssn\prod0\specimen_1210632453\ophys_session_1247774713\1247774713_stitched_full_field_img.h5"
Will catch up with @cbrrrry too spec out the skeleton of what QCing this image should be.
Carson (@cbrrrry ) and I talked yesterday and here is a skeleton of the QC for this image/file:
@nataliaorlova can you provide code that does 1?
For 2- if these items are evaluated manually (ie the operator looks by eye) can you please provide example images of the flag and failure modalities that you described above? I think we already have a controlled language tag and image for the bubbles but everything else is new
The code for finding the file, opening it and checking the fields? You guys should be able to do that in 5-10 lines of code...
As to #2 - let's start by visualizing the image to the operators - this is a new data stream, and we will be collecting examples as we have a way to look at them.
I have some rough code for this, part of which you have previously shared @nataliaorlova, that I am happy to provide. Would this live in data_access @DowntonCrabby ?
Okay had a brief meeting and here were the take-aways & tasks:
Proof of concept coding: Carson to provide code that does these tasks:
qc metric generation pipeline:
qc module creation & display in report
Just for visibility/clarity- we will try to incorporate this into the next milestone/release.
We are currently in the phase doing bug fixes on Milestone 2- so we're talking about this being in like milestone 3
I submitted a PR called " Fullfield qc #292 " with the code for this issue. Review at your leisure!
There are some cases where stitching was not good: E.g.: \allen\programs\mindscope\production\learning\prod0\specimen_1285648947\ophys_session_1305964574
Sometimes the fullfield is not stitched E.g.: \allen\programs\mindscope\production\learning\prod0\specimen_1292035016\ophys_session_1300393608
@DowntonCrabby @seanmcculloch I think this is still needed and should be prioritized as part of mouse QC / CO migration work
Full FOV 2P images are used for ophys-omfish registration and are going to start being generated by LIMS mesoscopes splitter module starting the week of Feb 13. We should think about how to QC them.
Example image can be found here
The file will be located at
$SESSION_OUTPUT_DIR/${session_id}_stitched_full_field_img.h5
. In the h5 file one can find a stitched full FOV 2P image and stitched full FOV 2P image with averaged surfaces inserted into it, along with the raw tiff metadata.Once the images are available we should review a few examples and discuss features/metrics to QC. First thoughts are: