Standard Morph

Standard Morph is a Python library designed for processing and validating SWC files. It provides tools for standardizing SWC structures and generating quality control (QC) reports. Future direction will include integration with backend databases.

Installation

coming soon:
pip install standard-morph

For now:
git clone https://github.com/AllenInstitute/standardmorph.git
cd standardmorph
pip install .

Usage

Example 1: Standardizing a Single SWC File

```python from standard_morph.Standardizer import Standardizer

Path to the SWC file

pathtoswc = './scratchfiles/1311509665_TT.ano.swc'

Initialize the Standardizer worker

worker = Standardizer( pathtoswc=pathtoswc, swcseparator=" ", somachildrendistancethreshold=50, validfilenameformat="None", somamipkwargs={} )

Validate the SWC file

worker.validate()

Write the QC'd SWC file with sorted node IDs

worker.writetoswc(outputswcpath="QCd_File.swc")

Generate an HTML report for the single cell

where nodedisplaymode='both' will write node ID and x,y,z coordinates

worker.reporttohtml(reportpath="CellQCReport.html", nodedisplay_mode='both')

Can inspect the report

This may be useful for writing the QC records to a database

print(worker.StandardizationReport)

{ 'inputfile': './scratchfiles/1311509665TT.ano.swc', 'StandardMorphVersion': '0.0.1', 'pathtomip': None, "errors": [ { "test": "SomaChildrenFurcation", "description": "Children nodes of the soma should not branch. The returned node IDs are immediate children of the soma that branch.", "nodeswitherror": [(2, 313.0, 4409.0, 8981.0)] }, { "test": "AxonOrigins", "description": "Axon should originate from a single location and should stem from axon, soma, or basal dendrite. Invalid axon origins are returned.", "nodeswitherror": [ (58, 3231.0, 3131.0, 9218.0), (423, 3521.0, 3320.0, 7840.0), (424, 3104.0, 3344.0, 8889.0), ] }, { "test": "DendriteOrigins", "description": "Each apical/basal dendritic node should have a parent node with type 1 (soma) or its respective dendrite type.", "nodeswitherror": [ (3, 310, 1310.0, 3044.0, 7742.0) , (15,530.0, 5502.0, 8173.0) ] } ], } ```

Example 2: Standardizing multiple SWC Files

```python

Define multiple SWC files

pathtoswc1 = "Vip-IRES-CreAi14IVSCC-259339.03.01.02678343034m.swc" pathtoswc2 = "Vip-IRES-CreAi14IVSCC-259339.03.01.02678343034m.swc"

allreports = [] for swcpath in [pathtoswc1, pathtoswc2]: worker = Standardizer(pathtoswc=swcpath, swcseparator=" ", somachildrendistancethreshold=50, validfilenameformat="None", somamipkwargs={}) worker.validate() thisreport = worker.StandardizationReport allreports.append(thisreport)

Generate a combined HTML report for multiple cells, display just the x,y,z coordinate

createhtmlreport(data=allreports, reportpath="MultiCellReport.html", nodedisplaymode='coord') ```

Example 3: Standardizing a Single SWC File + Soma MIP QC. UNTESTED

```python from standard_morph.Standardizer import Standardizer

Path to the SWC file

pathtoswc = 'Vip-IRES-CreAi14IVSCC-259339.03.01.02678343034_m.swc'

somamipkwargs = { "imagepath":"/soma/omezarr/image/", "outputdir":"/where/to/save/mip.png", "cropsize":128, "mipdepth":10 }

Initialize the Standardizer worker,

Note the validfilenameformat will check for AIND style regular expressions

worker = Standardizer( pathtoswc=pathtoswc, swcseparator=" ", somachildrendistancethreshold=50, validfilenameformat="AIND", somamipkwargs=somamipkwargs )

Validate the SWC file

worker.validate()

Generate an HTML report for the single cell

worker.reporttohtml(reportpath="SingleCellQCReportWithSomaMIP.html", nodedisplay_mode='coord') ```