I'm not entirely sure if this is a bug, feature request, or just me being naive in the Scan-image landscape.
I'm working on some data analysis routines that were previously done entirely in MATLAB. The data I'm working with heavily relies on Scan-image metadata that isn't readable from a standard .tiff reader, as explained here. My first problem arose from the ScanImageTiffReader.metadata() class method not actually giving me a serializable json object, it was single long string. So I had to parse it separetely first to access the metadata.
Then I found that the Scan-Image utility functions (or really any of their functions) haven't been implemented in the python bindings, namely data extractors like getMroiDataFromTiff().
I realize this specific issue may be more for appropriate for the ScanImageTiffReader devs, but my use-case for it is narrowly focused to usage with Suite2p. And I'm not sure its appropriate to ask/wait for them to implement just a few functions needed to extract the necessary data to analyze large 3D .tiff files.
Attempted alternative approaches:
I recreated some of the functionality that I needed out of the tiff reader. I have them on github here:
I'm wondering if generally people are just doing this metadata extraction part of the analysis in MATLAB, if there are other/better ways to do it, or if this functionality would be helpful to incorporate into the 'io' portion of Suite2p or ScanImageTiffReader.
It's also possible there are ways to do this already implemented, and I just haven't found them. Any thoughts would be appreciated on the topic.
FlynnOConnell
commented
1 year ago
Feature you'd like to see:
I'm not entirely sure if this is a bug, feature request, or just me being naive in the Scan-image landscape.
I'm working on some data analysis routines that were previously done entirely in MATLAB. The data I'm working with heavily relies on Scan-image metadata that isn't readable from a standard .tiff reader, as explained here. My first problem arose from the ScanImageTiffReader.metadata() class method not actually giving me a serializable json object, it was single long string. So I had to parse it separetely first to access the metadata.
Then I found that the Scan-Image utility functions (or really any of their functions) haven't been implemented in the python bindings, namely data extractors like getMroiDataFromTiff().
I realize this specific issue may be more for appropriate for the ScanImageTiffReader devs, but my use-case for it is narrowly focused to usage with Suite2p. And I'm not sure its appropriate to ask/wait for them to implement just a few functions needed to extract the necessary data to analyze large 3D .tiff files.
Attempted alternative approaches:
I recreated some of the functionality that I needed out of the tiff reader. I have them on github here:
Additional Context
I'm wondering if generally people are just doing this metadata extraction part of the analysis in MATLAB, if there are other/better ways to do it, or if this functionality would be helpful to incorporate into the 'io' portion of Suite2p or ScanImageTiffReader.
It's also possible there are ways to do this already implemented, and I just haven't found them. Any thoughts would be appreciated on the topic.