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docs: small fixes
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schlegelp committed Jan 18, 2021
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32 changes: 16 additions & 16 deletions docs/source/intro.rst
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Expand Up @@ -31,7 +31,7 @@ website for the paper, examples and data. Peter kindly shared skeletons derived
from the segmentation with the FAFB tracing community early on. These skeletons
were loaded into CATMAID instances by Tom Kazimiers and Eric Perlman.

To summarize, there are currently 4 "walled garden" FAFB CATMAID instances:
To summarize, there are currently 5 "walled garden" FAFB CATMAID instances:

1. The main instance at ``fafb/v14/`` (neuropil)
2. The first Google segmentation at ``fafb/v14-seg`` (neuropil)
Expand All @@ -47,12 +47,12 @@ segmentation of FAFB public as `"FlyWire" <https://flywire.ai/>`_.
Anyone can join this project but community guidelines similar to those for the
"walled garden" apply.

Important to note is that the FAFB image data was realigned for the flywire
Important to note is that the FAFB image data was realigned for the FlyWire
segmentation. This is why x/y/z coordinates typically vary by a micron or so
between original FAFB (also called "FAFB v14" or just "FAFB14") and flywire
between original FAFB (also called "FAFB v14" or just "FAFB14") and FlyWire
(also called "FAFB v14.1" or "FAFB14.1").

Deformation fields mapping between FAFB14 and flywire have been kindly provided
Deformation fields mapping between FAFB14 and FlyWire have been kindly provided
by the Seung lab.

Synaptic partner predictions
Expand All @@ -64,7 +64,7 @@ for FAFB (`Buhmann et al., 2019 <https://www.biorxiv.org/content/10.1101/2019.12

This data is effectively represented by pairs of x/y/z coordinates where one
coordinate is pre- and the other one is postsynaptic. In combination with either
the Google or the flywire segmentation, we can map these connections onto
the Google or the FlyWire segmentation, we can map these connections onto
neurons to compile connectivity tables.

The raw data is publicly available: see
Expand All @@ -77,32 +77,32 @@ Bringing it all together
------------------------
As the introduction above shows, there are various types of FAFB data (skeletons,
meshes, segmentations, synapses, synaptic partners) available on various
platforms (CATMAID, flywire and other web services) and in two different
spaces (FAFB14 and flywire/FAFB14.1).
platforms (CATMAID, FlyWire and other web services) and in two different
spaces (FAFB14 and FlyWire/FAFB14.1).

``FAFBseg`` and its R analog (`link <https://github.com/natverse/fafbseg>`_)
provide a single interface to draw from and combine all the FAFB data.

In particular, it enables you to:

- load flywire neurons (e.g. for visualization and analysis)
- skeletonize flywire neurons
- query connectivity for flywire or FAFB14 neurons
- transform data between FAFB14 and flywire
- move data between manual FAFB14, Google and flywire segmentation (experimental and subject to community guidelines!)
- load FlyWire neurons (e.g. for visualization and analysis)
- skeletonize FlyWire neurons
- query connectivity for FlyWire or FAFB14 neurons
- transform data between FAFB14 and FlyWire
- move data between manual FAFB14, Google and FlyWire segmentation (experimental and subject to community guidelines!)

General layout
**************
Currently, ``FAFBseg`` is divided into four main modules:

- ``fafbseg.flywire``: work with flywire segmentation
- ``fafbseg.flywire``: work with FlyWire segmentation
- ``fafbseg.google``: work with Google segmentation of FAFB14
- ``fafbseg.move``: import/export/move data around
- ``fafbseg.xform``: transform data between FAFB14 and flywire
- ``fafbseg.xform``: transform data between FAFB14 and FlyWire

You will find that certain functions have a version for Google and for flywire.
You will find that certain functions have a version for Google and for FlyWire.
For example, :func:`fafbseg.flywire.locs_to_segments` and
:func:`fafbseg.google.locs_to_segments` let you map locations to segmentation
IDs for the respective data set.

Check out the tutorials
Check out the tutorials
8 changes: 4 additions & 4 deletions docs/source/tutorials/flywire_secret.rst
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@@ -1,16 +1,16 @@
.. _set_flywire_secret:

Setting the flywire secret
Setting the FlyWire secret
==========================
Many data queries against flywire use ``cloudvolume`` which provides an
interface with flywire's chunkedgraph data base. To be able to query that
Many data queries against FlyWire use ``cloudvolume`` which provides an
interface with FlyWire's chunkedgraph data base. To be able to query that
backend you need to generate and save an API token (or "secret") similar to
CATMAID. This needs to be done only once.

Generate your secret
--------------------
Go to https://globalv1.flywire-daf.com/auth/api/v1/refresh_token and log in with
the account you use for flywire. You should then see a token that looks
the account you use for FlyWire. You should then see a token that looks
something like this:

.. code-block:: bat
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