Default KNIME workflow

ZIP-compressed default KNIME workflow for automated movie annotation, parameter extraction and result table assemby as detailed in Methods, section 'Data mining in CSV result files and assembly of final EXCEL result tables with KNIME'

raw movie data

ZIP-compressed hierarchical folder tree containing raw movie data as 16 bit TIFF image stack files. Each movie was acquired by fluorescence video microscopy on compartmentalized motor neurons cultured in Xona microfluidic chambers at standardized distal and proximal axonal readout positions at 3 frames per second with Lysotracker and Mitotracker. For more details refer to Methods, section ‘Live imaging of MN in MFCs’. The file path of the hierarchical folder tree defines the metadata of each movie (i.e. the experimental conditions of each movie) and serves as the base for the automated movie annotation with KNIME software, as detailed in Methods, section ‘Handling of meta data throughout the work flow’ and ‘Data mining in CSV result files and assembly of final EXCEL result tables with KNIME'

FIJI Morphology macro

FIJI macro code (ijm file) of static organelle morphology analysis as described in Methods, section 'Automated object recognition and static morphology analysis with the FIJI Morphology macro'

Z-scores

MS Excel table containing Z-scores of all parameters to build the multiparametric phenotypic signatures as described in the main manuscript under Methods, section 'Assembly of phenotypic HC signatures'

Dynamic Tracking Parameters

MS Excel result table containing all parameters of the dynamic organelle tracking analysis as described in the main manuscript under Methods, section 'Data mining in CSV result files and assembly of final EXCEL result tables with KNIME'

Axon Specificity

Illustration of absent dendrites at the distal and proximal readout position inside MFC microchannels. Representative example of Ctrl Mock iPSC-derived human spinal motor neurons matured over 3 weeks in MFCs showing IF immunostainings for the dendritic marker MAP2 (in pink) and the motor neuron marker SMI32 (turquoise). Note the absence of any MAP2-positive neurites inside channels at either the distal and proximal site where the movie acquisition was performed. Only a few MAP2-positive ramifications were reaching out from the open proximal field to the vicinity of proximal channel entries but remained outside. Scale bar = 10µm

Tracking Illustration

Illustration of the object recognition and tracking analysis. Representative examples of Ctrl, FUS and TDP43 axon images at the distal readout (Mock) obtained with Mitotracker (left) and Lysotracker (right), scale bar = 10µm. Note the high coverage of the FIJI Track Mate object recognition (pink circles) and tracking tool (yellow lines) as nearly every organelle is detected. White arrowheads point to examples of rare false positives outside microchannels that were removed through subsequent post filtering (track duration ≥ 3s, track displacement ≥ 1.2µm), see Methods, section ‘Automated object recognition and dynamic tracking with the FIJI Track Mate plugin’ and ‘Data mining in CSV result files and assembly of final EXCEL result tables with KNIME’

Static Morphology Parameters

MS Excel result table containing all parameters of the static organelle morphology analysis as described in the main manuscript under Methods, section 'Data mining in CSV result files and assembly of final EXCEL result tables with KNIME'