[BUG] Plotting SPCMs

[montanasamantzis]

** umiT version **: Bipolar v.2.0.0

Describe the bug
Unable to plot average maps (SPCMs) after running generate corr matrix function with yes to SPCMs. Issue saying Reference point is missing, but reference point (bregma), pixel size scale, logical mask, and ROIs have all been placed as per usual. Corr matrix runs generates fine as part of the process.

Screenshots

[BrunoOFSouza]

Hi @montanasamantzis ,
Is it possible to share the .mat file associated with the test_adam_MND--MND41--Baseline1_gcamp1_CtxImgfixednoisecutoff recording?

Thanks,

[montanasamantzis]

Hi Bruno,

I have emailed it since it wouldn't let me attach on Github. Please let me know if you need anything else! Thank you! :)

[BrunoOFSouza]

Hi @montanasamantzis ,

Thanks for the files. The SPCMap file is indeed lacking the reference point and pixel ratio information. Also, I noticed that the dataHistory of the file is lacking all processing steps after the importFromTIf function.
Could you describe exactly the steps that you took to generate the file (which functions at which order)? We will try to pinpoint the origin of the bug.

Thanks

[montanasamantzis]

Hi @BrunoOFSouza sorry I missed this reply!

For this data we had to do some additional cleaning steps so we performed image classification, hemo correction, and alignment before exporting the video as TIF to do some DF/F calculations and ICA. Following this we re-imported the corrected TIF into umIT which worked perfectly. Then following this the steps we performed were as follows:

• Generating ROI mask : place origin, set pixel scale, draw mask, adding Allen Atlas ROIs, save as ROI_mask.
• Generate correlation matrix: avg_vs_avg (i also tried centroid vs centroid), mean spatial, false z score, true spc map
• Plot SPC map (this is where the error appears)

[BrunoOFSouza]

Hi @montanasamantzis,
Thanks for the detailed description. Now, I am sure where the bug comes from.
Since the file was exported and re-imported to umIT, the pixel scale and origin coordinates were probably lost.
There is an extra step that you can do when you generate the ROI mask in the ROImanager app:

1. Open the re-imported .dat file either through DataViewer or umIToolbox app
2. Once you set the origin and pixel ratio parameters, click on the button Save Params to meta data file. This will embed the information in the imaging meta data file that will be passed along to the SPCmaps. Then, the PlotAvg tool will be able to access it.

This should fix the issue.

Please, let us know if the problem persists by re-opening this issue.