VolPy

Main features:

• Introducing VolPy a new module for analysis of voltage imaging data. A description of the analysis pipeline can be found in this preprint. An application on a dataset courtesy of the Svoboda lab can be found in demos/general/demo_pipeline_voltage_imaging.py.
• Introducing an additional algorithm for online analysis of 1p data, using a Ring-CNN based background model. An example is given in the notebook demos/notebooks/demo_ring_CNN.ipynb (GPU is required).

Other improvements:

• An eccentricity based test for component screening.
• Improved online analysis for 1p data (by fixing some bugs)
• Ability to analyze online arbitrary HDF5/MATv7.3 files.
• Ability to call merging directly from the estimates object.
• Improved docs.

Special thanks to @caichangjia for his work in integrating VolPy with CaImAn.

v1.7.1

Some bug fixes and small features including:

• Dealing with issue #678 (StopIteration exception prevention in Python 3.7)
• Changes in demo_online_CNMFE.ipynb
• Fixes a bug that was duplicating some work during pw-rigid motion correction
• Fixes a bug during motion correction for very short datasets issue #672
• Prevents NaN values from appearing when calling estimates.evaluate_components which was causing the cnm.save method to fail (issue #673)
• Native treatment of mat v7.3 files by treating them as hdf5 files.
• Memory efficient baseline removal through cm.base.movies.removeBL

1p online

Main features:

• Online processing of microendoscopic data (check demo_online_CNMFE.ipynb for an example. Dataset courtesy of the miniscope project).
• Fixed an old bug arising when resizing large movies using openCV
• Ability to make color movies when displaying the results
• Ability to perform motion correction only on a part of the FOV (and memory map only that part).
• Expose version using caiman.__version__
• Various other bug fixes and optimizations

v1.6.4

Pinning the tifffile package to 0.15.1

v1.6.3

This release addresses a bug mentioned in #651 occurring only for 2p data when ssub and tsub are not taking the same values.

v1.6.2

changes since last version:

• Fixed a bug occurring when computing the dimensions on a list of .avi files #636
• Introduced the parameter p_patch to automatically circumvent deconvolution when processing in patches without the need to change the parameter p #470

v1.6.1

This release reverts a couple of changes that were introduced in the past and where affecting the reproducibility of the eLife paper results. Thanks to @janden for introducing me to the amazing world of git bisect.

caimaconda

This release introduces several new features and contributions from many users:

• Ability to install CaImAn as a binary package through conda-forge. Thanks to @zbarry
• 3D motion correction (rigid and pw-rigid). Thanks to @as31
• Improvements in the GUI and integration with NWB files. Thanks to @bendichter and @caichangjia
• New notebook demos on seeding CNMF with binary masks and component registration across days. Thanks to @Hendriela
• Expanded method for cnmf.fit_file that allows complete analysis with one command. Thanks @HagaiHargil
• Some holoviews based visualization tools. Thanks to @phildong
• Expanded documentation, now based on readthedocs.

v1.5.3

Maintenance release fixing a couple of bugs:

• Fixed a numerical overflow bug occurring during memory mapping on some windows architectures #616
• Ask for the memory mapped file when using the GUI if the default location is not valid #590
• Fix a bug occurring during DF/F calculation for very short traces #613
• Fix a dimension swap bug when processing .avi files #609

scripts for dendritic data analysis and faster merging

New feature include:

• Implementation of the graph NMF method for analysis of dendritic data.
• A new notebook demo (dendritic_demo.ipynb) for dendritic data analysis.
• Faster merge iteration
• Option for merging in parallel, controlled from params.merging['parallel_merge'].
• Return correct residual during merging
• Ability for volumetric graph/sparse NMF
• Further robustness against NaNs
• Fixed some bugs for reading .sbx files #587
• More type annotations