v1.10.3

For this release:

• New logo
• Documentation is beginning to prefer the spelling "Caiman" over "CaImAn"
• Rearranged and fixed a lot of the docs functionality (this will be most visible on ReadTheDocs)
• Several notebook improvements (see #1263 for details)
• Images used in notebooks are now separate from those used by the docs, and are now distributed in their own subdir of the notebooks directory
• Made the link to Caiman Central more prominent
• Adjusted to upstream changes in new scipy release that broke our stats package
• Substantial code cleanups around how we do imports and some other things
• Fixed an infinite loop and some bad error messages

v1.10.2

Fixing a couple of glitches in most recent release.

• Images not showing.
• dff not calculating b/c scipy updates with deprecated functions.

v1.10.1

This is a minor release that only fixes an issue with conda-forge packaging that prevented package builds.

v1.10.0

Main changes for release 1.10.0

• Major revision to CNMF notebook

  • Patch visualization function added to help choose spatial parameters
  • More discussion of save/load results (including saving results to csv)
  • Emphasize key parameters
  • Sidebars added, with links to new deeper dive in docs (e.g., memmapping)
  • Explicit discussion of how dfof is calculated
  • Images of workflows
  • Discussion of handling large movies, and types of movies we can handle
  • Fix dfof so it handles denoised traces
  • Discussion of model and its visualization

• Major revision to CNMFE notebook

  • Discussion of ring model
  • Discussion of preprocessing filter and corr/pnr
  • Updated corr/pnr viewer and description of its use
  • Added visualization of bg noise

• Switch from z5py library to zarr library

• File format discussion added to docs

• Check for parameter consistency added between rf and gSiz (thanks @kushalkolar)

1.9.16

This release, which we are naming "Refreshing the Waters", has the following changes:

• Substantial reworking of many notebooks (and some split datasets useful for testing file lists)
• Documentation improvements throughout the code and elsewhere
• Remove some pins holding back holoviews, bokeh, and other jupyter components and some notebook reworking to handle upstream changes (hopefully fully fixing "no backend found" problems)
• Have caimanmanager (now without the .py) exposed as an entry point in both pip and conda packages, making life much easier for Windows users in particular
• Better handling of file lists in loading functions #1703
• A new way to display videos in notebooks using opencv #1080
• Other movie playing improvements #1101
• Smarter sparse nmf initialization
• Flesh out the existing intent to use pims as a fallback for loading avi files when platform-specific codec support for opencv is lacking, fix code for determining when to try this
• Fix an issue with numpy calls in online cnmf initialization #1102
• Move sandbox/ and scripts_labeling/ out of the checkout

1.9.15

In this release:

• Notebook for online processing of volumetric data (thanks to Johannes Friedrich).
• Notebook for voltage processing with VolPy added (thanks to Changjia Cai)
• Add related packages and video links to README (thanks to Kushal Kolar).
• Remove python2 relics such as old_div
• Multiple improvements to volumetric and online processing back end.
• Added OpenCV-based speedups to many filters.

1.9.14

In this release:

• We remove the use_cases/ directory from source releases (it is now available in a separate repo)
• Fixes for loading .mat files
• Some fixes for caiman_gui.py
• Fix motion correction for 3d mode
• Deal with upstream changes to scikit
• Deal with upstream changes to tensorflow
• For various notebooks deal with changed upstream packages

1.9.13

In this release:

• We pin holoviews because of upstream package compatibility issues
• Pull in some reworking of internal mmap paths (may break some external wrappers of caiman until they update)
• Remove use of a deprecated kwarg in sklearn's LassoLars (silencing very noisy warnings)
• Several mrcnn fixes (and a demo test), thanks to CaiChangjia
• Move off some deprecated python types, thanks to Johannes

1.9.12

In this release:

• Revise internal mmap filenames to make the code more robust in the long term
• Minor docs formatting and contents fixes
• Remove some unused code in notebooks, improve docs elsewhere
• (kushal kular): Fix dimension returns for tiff files written in append mode
• env var to override GPU selection
• Better error handling with CNMF params
• Utility functions for avi files, cropping
• Improved some error messages

1.9.11

This:

• Implements border_nan for other types of motion correction (thanks GBarnum)
• Moves a few unnecessary dynamic imports into being static
• Pins the minimal version of z5py and some other import issues to fix some oddities
• Fixes some old code that never worked correctly in view_components()
• Adds some warnings for not using APIs correctly
• Fixes #990
• Fixes some code in rolling_window() for some edge cases
• Adjusts to tifffile 2022.04.22
• Fixes an earlier refactor that broke a demo
• Fixes(?) #983
• Better handle file extensions
• Readme improvements
• Fixes for #959, #970, #971