suite2p - v0.14.6

What's Changed

• Cellpose-SAM support added
• Support for Python 3.11 and onwards added

- Jupyter Notebook
Published by chriski777 6 months ago

suite2p - v0.14.0

BinaryFile replaces BinaryRWfile as a class and has a method for writing tiffs (ie, for cropping and generating new tifs after loading in a dataset). PyNwb has also been added to the list of dependencies needed for testing.

Fixes the following issues: - #1007 ModuleNotFoundError with rastermap.mapping for GUI - #943: high pass filter documentation issue - #944 : File tifs naming issue with leading zeros - #991: Save_path0 documentation issue

- Jupyter Notebook
Published by chriski777 over 2 years ago

suite2p - v0.13.0

NOTE: right-click + drag now zooms the view; right-click once without dragging for cell flipping (CELL / NOT CELL)

Addresses the following bugs:

• #951: Adds .nd2 input to GUI
• #954: Adds sparse_detection mode to GUI
• #953: Fixes dependency issues with latest version of numpy and np.bool
• #930 : bin_frames has also been patched to accommodate cases in which current batch has fewer frames than bin_size.
• 4d9dd2b: Issue with numpy 1.24.4 in which np.asanyarray needs explicit input arguments
• #957: Removes scanimage-tiff-reader as a required dependency
• #955: Allows *.mesc files to be loaded with h5 option
• Fixes GUI zooming and panning from recent pyqtgraph update

New additions:

• Changes BinaryFile to use np.memmap for file reading/writing (~20% speed up)
• Adds yapf style guide

- Jupyter Notebook
Published by chriski777 almost 3 years ago

suite2p - v0.12.1

Fixes several bugs: - 2channel manual labeling #904 - Multiplane issue with NWB #905 - Saving Ops parameters with GUI #914 - Bad_frames issue with detection #908 - Non-rigid registration #907

Includes: - nd2 support.

- Jupyter Notebook
Published by chriski777 almost 3 years ago

suite2p - v0.12.0

Fixes the following bugs:

• scipy version keepdims issue
• badframes bug
• deprecated parameter pages removed from imread
• blocks registration issue when ops[nonrigid] set to false.

- Jupyter Notebook
Published by chriski777 about 3 years ago

suite2p - v0.11.1

suite2p can now handle numpy inputs to the main processing steps of the software! check out this notebook (thanks @chriski777!) with the exposed functions for registration, cell detection and ROI extraction.

- Jupyter Notebook
Published by carsen-stringer over 3 years ago

suite2p - v0.10.1

fixing some bugs in v0.10.0

Also removing mkl-fft dependency from library and replacing with pytorch fft's. Now suite2p can be installed from pip entirely

- Jupyter Notebook
Published by carsen-stringer over 4 years ago

suite2p - suite2p v0.10.0

Fixes bugs in v0.9 with cellpose integration

Adds several new features, outlined here: https://docs.google.com/presentation/d/1UDikmED-dG3zwXz2uyavRNr5sGzjas7wPbP4IjDQ3HY/edit#slide=id.p1

- Jupyter Notebook
Published by carsen-stringer almost 5 years ago

suite2p - suite2p v0.9.3

• fixed several bugs with multi-channel recordings including saving tiffs, aligning by 2nd channel, saving meanImgchan2 and saving Fchan2 and Fneu_chan2 in the merge GUI.
• added cellpose support to suite2p, run pip install cellpose in your suite2p environment and check out the ops['anatomical_only'] key.
• added support for optional default cell diameter
• fixed bruker tiff bug
• added ops['norm_frames'] (set to True by default) to decrease noise in registration
• added automated row removal for scanbox files

- Jupyter Notebook
Published by carsen-stringer about 5 years ago

suite2p - v0.9.2 suite2p

• removes a key which made ops.npy prohibitively large
• fixes a bug with loading NWB files
• fixes a bug with meanImg saving with aligntochan = 2
• fixes a bug with plane folder loading after folders have been moved

- Jupyter Notebook
Published by carsen-stringer over 5 years ago

suite2p - suite2p v0.9.0

• reorganization of tests
• addition of mesoscope tiff test
• removal of ops1 from pipeline and GUI
• new key ops['classfile'] that allows user to specify classifier used in pipeline
• removal of scikit-image dependency
• new key ops['multiplane_parallel'] to run planes simultaneously on a server

- Jupyter Notebook
Published by carsen-stringer over 5 years ago

suite2p - Suite2p v0.8.1

- Jupyter Notebook
Published by nickdelgrosso over 5 years ago

suite2p - Suite2p v0.8.0

- Jupyter Notebook
Published by nickdelgrosso over 5 years ago

suite2p - Suite2p v0.7.5

- Jupyter Notebook
Published by nickdelgrosso over 5 years ago

suite2p - Suite2p v0.7.1

• sparse_mode now default
• z-alignment in "view registered binary"
• manual labelling available
• merging (with alt+enter) and automated merge suggestions (particularly for dendritic/axonal recordings)
• scanbox support (no need to convert to h5)
• new ops['input_format'] which is a drop-down in the GUI

- Jupyter Notebook
Published by carsen-stringer about 6 years ago