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petersaj / Peters_et_al_CellReports_2022

Code used to produce figures in "Visuomotor learning promotes visually evoked activity in the medial prefrontal cortex", Peters et al., Cell Reports 2022.
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The code can`t run for lacking U_master and wf_roi #1

Open RenOdun opened 3 months ago

RenOdun commented 3 months ago

Thanks for sharing data and codes in github, but you perhaps forgot put some mat files here or I missed. The code can`t run for lacking some mat files in the first code file. load('C:\Users\Andrew\OneDrive for Business\Documents\CarandiniHarrisLab\analysis\wf_ephys_choiceworld\wf_processing\wf_alignment\U_master'); wf_roi_fn = 'C:\Users\Andrew\OneDrive for Business\Documents\CarandiniHarrisLab\analysis\operant_learning\wf_processing\wf_rois\wf_roi';

The 2nd question is the code"\AP_scripts_cortexlab-master\load_and_process\widefield\AP_preprocess_widefield_pco.m". It may be the first processing step for tiff picture, and I didn`t find next steps for removing the hemodynamic effects on fluorescence and others, because there is no other code file containd a parameter named "Vrec", which is only used in 'AP_preprocess_widefield_pco.m'.

The code "AP_preprocess_widefield_pco.m" seems to be independent from other codes, because in other codes, parameter "U" and "V" were loaded by function "readUfromNPY" and "readVfromNPY" in code "AP_load_experiment.m", and those subfunctions did not exist in your github files but in the https://github.com/cortex-lab/widefield.

Your codes seems to be mixed with many incompatible and incomplete versions from different periods, and I`d appreciate it if you could apply complete codes here.

petersaj commented 3 months ago

Thanks for pointing out: I've now uploaded U_master and wf_roi into the OSF repository (https://osf.io/2wh5v/) with short descriptions on the wiki.

I've also put notes in the Github and OSF repositories that the card-coded paths to load U_master and wf_roi will need to be changed by the user to point to where these files are stored locally.

For AP_preprocess_widefield_pco: that this function and other preprocessing-related functions are not related to this repository (which is dedicated to figure code for this paper), and are not maintained for general use (I no longer use this camera or code).

I'm happy to answer questions or point you to other code if it helps though, if you can tell me more about how you're trying to use this function? Vrec is the temporal components from SVD for that particular recording, which was saved onto our server according to our conventions. If you'd like to see the context for how that was used, see this script for batch preprocessing widefield data: lilrig_batch_widefield

Note also AP_preprocess_widefield_pco is not part of the process for correcting hemodynamics: this function performs SVD on each color separately, and then another function HemoCorrectLocal performs the hemodynamic correction.