v0.7.2

This release contains fixes from the master branch as of May 30, 2022 that have been back-ported onto v0.7 so that they can run in python3.6, and within the Mesmerize VM. This will probably be the last release.

Changes

• use imagej=False when saving tiff files, see #78
• option to keep memmap files for caiman stuff, "Use work dir" Must be unchecked in batch manager for this
• ptime fix, see #84
• .btf file associations for big tiff
• some ROI manager bugs for 3d stuff
• xmltodict is required

v0.8.0

New

• Import .isxd movies aquired by inscopix acquisition software (requires python>=3.8)
• Import freehand & circular ImageJ ROIs

v0.7.1

Fixed

• Fix sampling rate calculation for OME meta data import

v0.7.0

New

• Import OME XML meta data stored in tiff files

Fixed

• use latest pandas required by latest pynwb and latest hdmf due to numpy 1.20, see NeurodataWithoutBorders/pynwb#1363
• fix #55, don't move logfiles to zipfile in windows
• bugfix 88edbd3 so custom modules are imported properly

v0.6.1

Fixed

• bug in mesmerize.__main__ where old logfiles weren't being moved into zipfile
• memmaps can't be removed on Windows (see #54), temporary fix added for CNMFE (already exists for other caiman modules)

v0.6.0

New

• Allow installation on python >3.6
• Logger outputs all stdout and tracebacks for exceptions to logfiles

Modified

• @present_exception() windows print traceback in a scrollable box
• args to mesmerize.__main__ are now handled using click instead of sys.argv
• use webgl backend for bokeh datapoint tracer's image viewer
• continued work on bokeh-based plots, continued work on displaying ROIs in bokeh datapoint tracer
• StimulusExtraction flowchart node gives informative messages if there are issues with samples

Fixed

• matplotlib-related bugfix when opening CNMFE batch items
• mcorr projections bugfix when comparing <3 batch items
• bugfix when opening saved stim tuning plots

v0.5.1

Fixed

• Project Browswer will display the offending project column if there is an issue in loading it.
• Index error with importing CNMF files (see #50)

v0.5.0

Modified

• PeakFeatures node will provide warnings instead of exceptions when there are issues w.r.t. a specific peak, such as missing bases or index errors. The offending peaks are ignored, and the the user is provided with information that they can use to check the offending peaks.

Fixed

• Windows multiprocess fork issues with CNMF runner modules.
• Use sklearn~=0.23.1 due to tslearn compatibility
• Use psutil v5.8 instead of v5.7 due to issues on the latest version of mac os
• Davies-Bouldin function fixed

v0.4.1

Fixed

• Use of scalers in Neural Decompose plot
• add_roi() addressing a nonexistent viewer function for various backend managers.

v0.4.0

New

• Bokeh based plots that use a bokeh-based datapoint tracer, still in very early stages
• k-Shape "gridsearch", select a n-partitions range and number of combinations, returns heatmap of all k-Shape runs with inertia values
  NOTE: The gridsearch is not saved when the plot is saved. Only the chosen kshape iteration will be saved. This will be fixed in a future release
• Plot neural dynamics in PCA or LDA space
• PadArrays flowchart node to pad dataframe arrays when sizes don't match, useful when splicing is undesired
• View mean, max, or std projection of caiman motion correction outputs by selecting them from the batch manager

Modified

• CNME Viewer module uses CNMFParams when running batch items instead of passing the params are args directly to CNMF.__init__()
• Improved performance when importing a project dataframe in the flowchart
• The project curves dir is deprecated. Backwards compatibility is maintained
• Project browser supports filtering of list-type columns, such as stimulus/behavioral names
• Use tslearn v0.4
• Lots of bug fixes everywhere
• Fix finding (newer?) CUDA GPUs
• Fix bug with stimtuning plot if only one stim type is present