External software packages

The folder _external_programs is for external software packages or algorithms used by CIAtah. These are automatically downloaded when running obj.setup; after creating a CIAtah object by calling obj = CIAtah; or directly by running ciapkg.io.loadDependencies();.

The following programs will be found in this folder after downloading (e.g. after running ciapkg.io.loadDependencies):

• GUI and display
  • ImageJ/Fiji - Miji to allow calling of ImageJ/Fiji, only download mij.jar and ij.jar. https://imagej.net/plugins/miji.
• Cell extraction
  • CELLMax - Will be made public upon publication.
  • CNMF - https://github.com/flatironinstitute/CaImAn-MATLAB.
  • CNMF-E - https://github.com/zhoupc/CNMF_E.
  • CVX - http://cvxr.com/cvx/download/ (e.g. http://web.cvxr.com/cvx/cvx-rd.zip).
  • EXTRACT - https://github.com/schnitzer-lab/EXTRACT-public.
• NWB
  • nwb_schnitzer_lab - https://github.com/schnitzer-lab/nwb_schnitzer_lab.
  • yamlmatlab - https://github.com/ewiger/yamlmatlab.
  • matnwb - https://github.com/NeurodataWithoutBorders/matnwb.
• File I/O
  • Bio-Formats - MATLAB version at https://www.openmicroscopy.org/bio-formats/downloads/.
• Motion correction
  • Turboreg - C and MEX function implementation of http://bigwww.epfl.ch/thevenaz/turboreg/.
  • NoRMCorre - https://github.com/flatironinstitute/NoRMCorre.
  • PatchWarp - https://github.com/ryhattori/PatchWarp.

Direct download

Direct download links for cases in which users are having connectivity issues. Extract and place contents in folder in the _external_programs named as indicated:

• cnmfe - https://github.com/bahanonu/CNMF_E/archive/master.zip
• cnmf_current - https://github.com/flatironinstitute/CaImAn-MATLAB/archive/master.zip
• extract - https://github.com/schnitzer-lab/EXTRACT-public/archive/master.zip
• cvx_rd - http://web.cvxr.com/cvx/cvx-rd.zip
• imagej
  • http://bigwww.epfl.ch/sage/soft/mij/mij.jar
    • Backup URL: http://tiny.ucsf.edu/3wFyol
  • http://rsb.info.nih.gov/ij/upgrade/ij.jar
• bfmatlab - https://downloads.openmicroscopy.org/bio-formats/6.6.1/artifacts/bfmatlab.zip
• nwbpkg - https://github.com/schnitzer-lab/nwbpkg/archive/master.zip
• yamlmatlab - https://github.com/ewiger/yamlmatlab/archive/master.zip
• matnwb - https://github.com/NeurodataWithoutBorders/matnwb/archive/v2.2.5.3.zip
• gramm - https://github.com/piermorel/gramm/archive/master.zip
• turboreg - http://tiny.ucsf.edu/ciatahTurboreg
• cocoapi - https://github.com/cocodataset/cocoapi
• patchwarp - https://github.com/ryhattori/PatchWarp using my fork https://github.com/bahanonu/PatchWarp