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first implementation of bandsilo and band scan annotation - #11

Merged
m-xie merged 55 commits into
mainfrom
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Oct 22, 2026
Merged

first implementation of bandsilo and band scan annotation#11
m-xie merged 55 commits into
mainfrom
dev

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@m-xie m-xie commented Oct 22, 2026

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m-xie and others added 30 commits July 15, 2026 01:39
@m-xie
add/update dependencies for bandsilo
8b61529
@m-xie
implemented h5 loaders, basic dmd geometry functions, and parameters
ac1025a
@m-xie
add code for params gui and user roi selection gui
9d00181
@m-xie
implement functions for loading lowres slap2 data
a81767c
@m-xie
add VS Code directory to .gitignore
bc6e97e
@m-xie
implement activity image generation for bandscan
ebb52dc
@m-xie
fix bug in comment format
7a78993
@m-xie
implement source localization step of bandsilo
6a45d8b
@m-xie
implement lowres nmf
3180d14
@m-xie
implement high-res trace extraction
6c60398
@m-xie
implement run code for bandsilo
a709a5a
@m-xie
separate out annotations and fix trialtable
4f1dcfa
@m-xie
add verbose mode
da7e776
@m-xie
set default analyze_hz
a7c2fc7
@m-xie
fix new pandas read-only issue
69dda2c
@m-xie
use middle pixel as reference pixel in a band
72e1918
@m-xie
add missing default parameters
e4aa69c
@m-xie
restrict locations of final sources closer to peak
eaff16c
@m-xie
add debugging feature to process only the first few trials
577def7
@m-xie
update dmd data reading bar progress bar
013e227
@m-xie
add bottleneck dependency and update rolling baseline to use median
f3fc3f7
@m-xie
fix sign issue when applying motion estimates
8105ad3
@m-xie
fix issue with double PSF convolution when doing matched filter
7e780f0
@m-xie
modify median subtraction
aba7b8d
@m-xie
use cubic interpolation as default for calculating background
775eea6
@m-xie
assume single pixel-sized sources for matched filter
89f29dc
@m-xie
revert to difference of gaussian filter
0d20e9a
@m-xie
remove band artifact by median filtering along the superpixel pattern
fa8504a
@m-xie
remove edge artifacts
0bca3be
@m-xie
remove mad normalization of activity image
ad8d61f
m-xie and others added 25 commits September 10, 2026 07:31
@m-xie
allow anisotropic peak fitting in activity image
57e6d83
@m-xie
change default peakth
a0c908a
@m-xie
print number of detected sources
846c772
@m-xie
restrict size of final spatial profiles
3259392
@m-xie
refactor package to reorganize and rename files
3a3d54a
@m-xie
fix background_interpolation to always be cubic
b46039a
@m-xie
remove num_channels and activity_channel parameters
66b3a39
@m-xie
remove operator parameter
6325551
@m-xie
allow activity image peak threshold to vary between ROIs
c5d29bb
@m-xie
add z-tolerance parameter
fb148c7
@m-xie
update z-tolerance in all steps
7ca8fe9
@m-xie
conduct nmf on temporally matched filtered signal
819f9a4
@m-xie
make temporal filter before nmf nan-aware
f7559eb
@m-xie
add option to do simple weighted average trace extraction
fe64739
@m-xie
replace least squares solvel with mldivide-style algorithm
a610ff0
@m-xie
fix handling of nonfinite frames in trace extraction
25f0340
@m-xie
add denoised fitting of final temporal traces
9c1e1b8
@m-xie
exclude soma from peak detection
ab5236d
@m-xie
update F0 to be a projection into the background
ab48fb8
@m-xie
allow setting of random seed
1d1b5fb
@m-xie
update documentation
31faeee
@m-xie
clean up some unused parameters in background estimation
1549438
@m-xie
remove unvetted unit tests
7cffab5
@m-xie
clean up remants of removed unittests
6b929a8
@m-xie
fix formatting
5dc4d10
@m-xie m-xie self-assigned this Oct 22, 2026
@m-xie
m-xie merged commit 42978af into main Oct 22, 2026
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