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

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

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.

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.

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.

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

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

suite2p v0.9.3

• fixed several bugs with multi-channel recordings including saving tiffs, aligning by 2nd channel, saving meanImg_chan2 and saving F_chan2 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

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 align_to_chan = 2
• fixes a bug with plane folder loading after folders have been moved

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