MagellanMapper v1.0 Release Notes#

MagellanMapper v1.0.0#

Changes#

Installation

  • Updated requirements and environment scripts

GUI

  • More zoom levels in ROI editor

  • Customize position of ROI with overview plots

CLI

  • More CSV manipulations by command-line: append columns to a CSV, normalize metrics

  • Generate generic line plots including error bars

Atlas refinement

  • Increase default smoothing for P14 atlas

Atlas registration

  • Increase bspline grid size when using correlation coefficient

I/O

  • Specify alternate metadata files by --meta command-line argument

  • Load blobs directly rather than through image setup

Python stats and plots

  • Nuclei clustering stats using DBSCAN and k-nearest-neighbors from scikit-learn

  • further customize generic bar plots

  • Option to draw a horizontal line on bar plots based on a summary function

  • Option to show labels as a binary image

  • Fix DSC measurements for labels

R stats and plots

  • Record n for each subgroup

  • Profile for basic stats

Dependency Updates#

Python Dependency Changes#

  • Scikit-learn for clustering