1.8.1

• Remove keras from list of dependencies to avoid problems arising sometimes in windows installations #702 This does not affect the codebase unless you want to use the VolPy module for analyzing voltage imaging data. In this case, you would need to install keras by entering your environment and typing
  conda install keras -c conda-forge
• Turn the GUI into binary and make it accessible through the caiman_data folder #700
• Fix a bug occurring sometimes when plotting contours in a notebook #699

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