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catalystneuro
/
roiextractors
Python-based module for extracting from, converting between, and handling optical imaging data from several file formats. Inspired by SpikeInterface.
https://roiextractors.readthedocs.io/en/latest/index.html
BSD 3-Clause "New" or "Revised" License
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Add `depth_slice()` to ImagingExtractors
#231
weiglszonja
closed
7 months ago
5
Update `BrukerTiffImagingExtractor`
#230
weiglszonja
closed
1 year ago
6
Refactor `NwbImagingExtractor` to support extracting data from `OnePhotonSeries`
#229
weiglszonja
closed
1 year ago
1
[Feature]: Import mean or summary images from all segmentation methods
#228
RichieHakim
closed
9 months ago
5
allow for incomplete data ingestion, fix ypix bug, add mean image to caiman seg class
#227
RichieHakim
closed
9 months ago
11
Update feature request form
#226
CodyCBakerPhD
closed
1 year ago
0
Add `MiniscopeImagingExtractor`
#225
weiglszonja
closed
1 year ago
7
[Feature]: Allow for incomplete data ingestion
#224
RichieHakim
closed
8 months ago
4
Rename `MicroManagerTiffImagingExtractor` channel to 'OpticalChannelDefault'
#223
weiglszonja
closed
1 year ago
3
Add `MicroManagerTiffImagingExtractor`
#222
weiglszonja
closed
1 year ago
2
[pre-commit.ci] pre-commit autoupdate
#221
pre-commit-ci[bot]
closed
1 year ago
0
add `BrukerTiffImagingExtractor`
#220
weiglszonja
closed
1 year ago
13
[pre-commit.ci] pre-commit autoupdate
#219
pre-commit-ci[bot]
closed
1 year ago
1
[pre-commit.ci] pre-commit autoupdate
#218
pre-commit-ci[bot]
closed
1 year ago
0
[pre-commit.ci] pre-commit autoupdate
#217
pre-commit-ci[bot]
closed
2 years ago
0
Add detector for if timestamps are set
#216
CodyCBakerPhD
closed
2 years ago
1
Debug masks for SubFrameSegmentation
#215
CodyCBakerPhD
closed
2 years ago
2
[pre-commit.ci] pre-commit autoupdate
#214
pre-commit-ci[bot]
closed
2 years ago
0
Enable `generate_dummy_segmentation_extractor` to generate voxel masks
#213
h-mayorquin
opened
2 years ago
0
Relax rounding of frame_to_time()
#212
CodyCBakerPhD
closed
2 years ago
3
[pre-commit.ci] pre-commit autoupdate
#211
pre-commit-ci[bot]
closed
2 years ago
0
ExtractSegmentationExtractor improvements
#210
weiglszonja
closed
2 years ago
3
Avoid duplication of functionality to retrieve traces in segmentation extractor
#209
h-mayorquin
opened
2 years ago
2
Debugs for the NWBSegmentationExtractor
#208
CodyCBakerPhD
closed
2 years ago
6
Finish correcting segmentation orientation
#207
CodyCBakerPhD
closed
2 years ago
2
Suite2pSegmentationExtractor still uses (num_rois, num_frames) format for its traces
#206
h-mayorquin
closed
2 years ago
2
Make `toy_example.py` dependency on spikeextractors clearer
#205
h-mayorquin
closed
2 years ago
6
Finalize droping `spikextractors`, remove its use in `toy_example.py`
#204
h-mayorquin
opened
2 years ago
1
Debug to edge case of MultiImaging
#203
CodyCBakerPhD
closed
2 years ago
4
Unify terminology for frames in `frame_to_time` and `get_frame`.
#202
h-mayorquin
opened
2 years ago
3
[Merge after #200]: Subframe segmentation
#201
CodyCBakerPhD
closed
2 years ago
2
Fix segmentation orientation
#200
CodyCBakerPhD
closed
2 years ago
1
Make external dependencies imported lazy
#198
CodyCBakerPhD
closed
2 years ago
1
Pull data from S3 bucket
#197
CodyCBakerPhD
closed
2 years ago
1
Remove spikeextractors dependency
#196
CodyCBakerPhD
closed
2 years ago
2
Improvements to MultiImagingExtractor
#195
CodyCBakerPhD
closed
2 years ago
7
[Fix] get segmentation images in `NewExtractSegmentationExtractor`
#194
weiglszonja
closed
2 years ago
0
Floats comparison on numpy array requieres `assert_allclose`
#193
h-mayorquin
closed
7 months ago
2
Follow-up on `ExtractSegmentationExtractor`
#192
weiglszonja
closed
2 years ago
1
[refactor] `NwbSegmentationExtractor`
#191
weiglszonja
closed
2 years ago
4
[refactor] Testing SegmentationExtractor images
#190
weiglszonja
closed
2 years ago
2
[Discussion]: Unifying tests for SegmentationExtractor?
#189
weiglszonja
opened
2 years ago
4
`SegmentationExtractor`: add `set_times`
#188
weiglszonja
closed
2 years ago
3
`SegmentationExtractor`: add frame_to_time, get_roi_ids as class methods
#187
weiglszonja
closed
2 years ago
4
Remove squeezing frames in get_frames for `MultiImagingExtractor`
#186
weiglszonja
closed
2 years ago
3
[Discussion] Inconsistencies in `SegmentationExtractor`s
#185
weiglszonja
closed
2 years ago
2
[Documentation]: Add API docs
#184
bendichter
closed
6 months ago
2
[Feature]: Port over GPL-licensed extractors
#183
CodyCBakerPhD
opened
2 years ago
0
Release 0.4.18
#182
h-mayorquin
closed
2 years ago
0
Test spikeinterface-like behavior for get_video with one element
#181
h-mayorquin
closed
2 years ago
4
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