@ pcdl : in the middle of updating the man pages.

Author: elmbeech

man/TUTORIAL_neuroglancer.md

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+# PhysiCell Data Loader Tutorial: pcdl and Neuroglancer.
+
+[Neuroglancer](https://research.google/blog/an-interactive-automated-3d-reconstruction-of-a-fly-brain/) is a [WebGL](https://en.wikipedia.org/wiki/WebGL)-based viewer for volumetric data.
+It is capable of displaying arbitrary (non axis-aligned) cross-sectional views of volumetric data, as well as 3-D meshes and line-segment based models (skeletons).
+
+[Ome.tiff](https://www.openmicroscopy.org/ome-files/) is the open microscopy image standard format used by wet lab scientists to store (fluorescent) microscopy data.
+
+In 2022, in the middle of the pandemic, a small group of programmers undertook at the Image Analysis Working Group of the Cancer Systems Biology Consortium & Physical Sciences-Oncology Network [hackathon](https://github.com/IAWG-CSBC-PSON/hack2022-10-neuroglancer) the endeavor to write a python3 script that directly can render ome.tiff files into Neurogalncer.
+This script was adapted for the pcdl project.
+
+
+### ✨ command line
+
+With pcdl it is very easy to generate time step and time series ome.tiff files from regular PhysiCell output straight from the command line and render them into Neuroglancer.
+
+#### command line time step
+Generate time step 6 ome.tiff
+
+```bash
+pcdl_make_ome_tiff pcdl_make_ome_tiff output_2d/output00000006.xml
+```
+
+Render time step 6 ome.tiff
+
+```bash
+pcdl_render_neuroglancer output_2d/output00000006_oxygen_water_default_blood_cells_ID.ome.tiff
+```
+
+#### command line time series
+
+Generate time series ome.tiff
+
+```bash
+pcdl_make_ome_tiff output/
+```
+
+Render timer series time step 0.
+
+```bash
+pcdl_render_neuroglancer output/timeseries_oxygen_water_default_blood_cells_ID.ome.tiff
+```
+
+Render time series time step 12.
+
+```bash
+pcdl_render_neuroglancer output/timeseries_oxygen_water_default_blood_cells_ID.ome.tiff 12
+```
+
+#### command line man pages
+
+```bash
+pcdl_make_ome_tiff -h
+```
+```bash
+pcdl_render_neuroglancer -h
+```
+
+### ✨ python
+With pcdl it is very easy to generate within python3 time steps and time series ome.tiff files from regular PhysiCell output and render them into Neuroglancer.
+
+#### python time step
+
+Generate and directly render time step 6.
+```python
+import pcdl
+
+mcds = pcdl.TimeStep('output_2d/output00000006.xml')
+mcds.render_neuroglancer(mcds.make_ome_tiff())
+```
+
+#### python time series
+
+Generate time series, then render.
+```python
+import pcdl
+
+mcdsts = pcdl.TimeSeries('output_2d/')
+s_pathfile = mcdsts.make_ome_tiff()
+mcdsts.render_neuroglancer(s_pathfile)  #  time step 0
+```
+```python
+mcdsts.render_neuroglancer(s_pathfile, 12)  #  time step 12
+```
+
+#### python docstrings
+
+```python
+import pcdl
+help(pcdl.render_neuroglancer)
+```
+
+### ✨ Further readings
+
+Please work through the official documentation to learn how to run the Neuroglancer software.
++ https://github.com/google/neuroglancer
++ https://neuroglancer-docs.web.app/index.html
++ https://research.google/blog/an-interactive-automated-3d-reconstruction-of-a-fly-brain/
+
+That's it. The rest is analysis within neuroglancer!