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EIN-lab / CHIPS

CHIPS, or Cellular and Hemodynamic Image Processing Suite, is an open-source MATLAB toolbox designed to analyse functional images of cells and blood vessels, primarily from two-photon microscopy. Please see the README file, which is displayed at the bottom of this page, for more information.
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Support Newer ScanImage TIFs #8

Open HagaiHargil opened 3 years ago

HagaiHargil commented 3 years ago

Resolves #2.

This PR introduces support for TIFs generated with newer files - either V5 or V2016+. This means that users may now use the built in SCIM_Tif class when reading SI TIFs instead of manually constructing them with RawImageDummy.

I have an SI5 TIF ready for testing, and as you see I added it to the tests file, but I'm not sure how you would like to include it "officially". I will also add a SI2020 file to the mix.

pbl007 commented 3 years ago

Do we still need to have a CalibrationPixelSize file for each obj/mag?

HagaiHargil commented 3 years ago

It's for each objective, yes, because that's how you factor in the FOV in um, I believe. The zoom\mag part is done automatically, so it's basically a single file per lens, and the user has to manually choose the calibration file. A wrapper script can take care of that, assuming the objective is usually the same.