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first implementation of bandsilo and band scan annotation - #11

Merged

m-xie merged 55 commits into

mainfrom

dev

Oct 22, 2026

Merged

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

Commits on Jul 15, 2026
- add/update dependencies for bandsilo
  m-xie
  committed
  8b61529
Commits on Jul 16, 2026
- implemented h5 loaders, basic dmd geometry functions, and parameters
  m-xie
  committed
  ac1025a
- add code for params gui and user roi selection gui
  m-xie
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  9d00181
- implement functions for loading lowres slap2 data
  m-xie
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  a81767c
- add VS Code directory to .gitignore
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  bc6e97e
Commits on Jul 26, 2026
- implement activity image generation for bandscan
  m-xie
  committed
  ebb52dc
- fix bug in comment format
  m-xie
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  7a78993
Commits on Jul 27, 2026
- implement source localization step of bandsilo
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  6a45d8b
Commits on Jul 28, 2026
- implement lowres nmf
  m-xie
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  3180d14
- implement high-res trace extraction
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  6c60398
- implement run code for bandsilo
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  a709a5a
Commits on Aug 6, 2026
- separate out annotations and fix trialtable
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  4f1dcfa
Commits on Aug 7, 2026
- add verbose mode
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  da7e776
- set default analyze_hz
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  a7c2fc7
- fix new pandas read-only issue
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  69dda2c
Commits on Aug 8, 2026
- use middle pixel as reference pixel in a band
  m-xie
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  72e1918
- add missing default parameters
  m-xie
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  e4aa69c
Commits on Aug 10, 2026
- restrict locations of final sources closer to peak
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  eaff16c
Commits on Aug 26, 2026
- add debugging feature to process only the first few trials
  m-xie
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  577def7
- update dmd data reading bar progress bar
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  013e227
Commits on Aug 28, 2026
- add bottleneck dependency and update rolling baseline to use median
  m-xie
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  f3fc3f7
- fix sign issue when applying motion estimates
  m-xie
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  8105ad3
Commits on Aug 31, 2026
- fix issue with double PSF convolution when doing matched filter
  m-xie
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  7e780f0
- modify median subtraction
  m-xie
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  aba7b8d
Commits on Sep 2, 2026
- use cubic interpolation as default for calculating background
  m-xie
  committed
  775eea6
Commits on Sep 3, 2026
- assume single pixel-sized sources for matched filter
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  89f29dc
Commits on Sep 4, 2026
- revert to difference of gaussian filter
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  committed
  0d20e9a
Commits on Sep 9, 2026
- remove band artifact by median filtering along the superpixel pattern
  m-xie
  committed
  fa8504a
- remove edge artifacts
  m-xie
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  0bca3be
- remove mad normalization of activity image
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  ad8d61f
Commits on Sep 10, 2026
- allow anisotropic peak fitting in activity image
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  57e6d83
Commits on Sep 11, 2026
- change default peakth
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  a0c908a
- print number of detected sources
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  846c772
- restrict size of final spatial profiles
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  3259392
Commits on Sep 21, 2026
- refactor package to reorganize and rename files
  m-xie
  committed
  3a3d54a
- fix background_interpolation to always be cubic
  m-xie
  committed
  b46039a
- remove num_channels and activity_channel parameters
  m-xie
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  66b3a39
- remove operator parameter
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  6325551
Commits on Sep 29, 2026
- allow activity image peak threshold to vary between ROIs
  m-xie
  committed
  c5d29bb
Commits on Sep 30, 2026
- add z-tolerance parameter
  m-xie
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  fb148c7
- update z-tolerance in all steps
  m-xie
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  7ca8fe9
Commits on Oct 1, 2026
- conduct nmf on temporally matched filtered signal
  m-xie
  committed
  819f9a4
- make temporal filter before nmf nan-aware
  m-xie
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  f7559eb
- add option to do simple weighted average trace extraction
  m-xie
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  fe64739
Commits on Oct 2, 2026
- replace least squares solvel with mldivide-style algorithm
  m-xie
  committed
  a610ff0
- fix handling of nonfinite frames in trace extraction
  m-xie
  committed
  25f0340
Commits on Oct 9, 2026
- add denoised fitting of final temporal traces
  m-xie
  committed
  9c1e1b8
Commits on Oct 20, 2026
- exclude soma from peak detection
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  committed
  ab5236d
Commits on Oct 22, 2026
- update F0 to be a projection into the background
  m-xie
  committed
  ab48fb8
- allow setting of random seed
  m-xie
  committed
  1d1b5fb
- update documentation
  m-xie
  committed
  31faeee
- clean up some unused parameters in background estimation
  m-xie
  committed
  1549438
- remove unvetted unit tests
  m-xie
  committed
  7cffab5
- clean up remants of removed unittests
  m-xie
  committed
  6b929a8
- fix formatting
  m-xie
  committed
  5dc4d10

Commits

Commits on Jul 15, 2026

Commits on Jul 16, 2026

Commits on Jul 26, 2026

Commits on Jul 27, 2026

Commits on Jul 28, 2026

Commits on Aug 6, 2026

Commits on Aug 7, 2026

Commits on Aug 8, 2026

Commits on Aug 10, 2026

Commits on Aug 26, 2026

Commits on Aug 28, 2026

Commits on Aug 31, 2026

Commits on Sep 2, 2026

Commits on Sep 3, 2026

Commits on Sep 4, 2026

Commits on Sep 9, 2026

Commits on Sep 10, 2026

Commits on Sep 11, 2026

Commits on Sep 21, 2026

Commits on Sep 29, 2026

Commits on Sep 30, 2026

Commits on Oct 1, 2026

Commits on Oct 2, 2026

Commits on Oct 9, 2026

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Commits on Oct 22, 2026