Morphology Files
Each mask must be binary (i.e., white pixels (‘1’) for the segmented
tissue and black pixels (‘0’) elsewhere) and must use Tagged Image File
Format (i.e., .tif
, or .tiff
). All masks must be defined within the same
field of view, be the same size, and be the same resolution. To convert
between pixels of the input masks to dimensioned length (micrometers), the user must specify
a “ScaleInputMode”
in Sample (S7 and S8 Text). If using the mask input mode, a mask for the scale bar (s.tif
) of known length (oriented horizontally) must be provided (see “Scale Bar” in Fig 2) and the length of the scale
bar must be indicated in Sample (S7 and S8 Text). If using the ratio input mode, the user explicitly specifies the micrometers/pixel of the input masks in Sample (S7 and S8 Text), and no scale bar image is required.
The user is required to set the “MaskInputMode”
in Sample
(“mask_input”
) to communicate the contents of the segmented histology
files (S7 and S8 Text). Ideally, segmented images of boundaries for both the “outers”
(o.tif
) and “inners” (i.tif
) of the perineurium will be provided, either
as two separate files (o.tif
and i.tif
) or combined in the same image
(c.tif
) (see “Inners”, “Outers”, and “Combined” in Fig 2). However, if
only inners are provided—which identify the outer edge of the
endoneurium—a surrounding perineurium thickness is defined by the
“PerineuriumThicknessMode”
in Sample
(“ci_perineurium_thickness”
); the thickness is user-defined,
relating perineurium thickness to features of the inners (e.g., their
diameter). It should be noted that defining nerve morphology with only
inners does not allow the model to represent accurately fascicles
containing multiple endoneurium inners within a single outer perineurium
boundary (“peanut” fascicles; see an example in Fig 2); in this case,
each inner trace will be assumed to represent a single independent
fascicle that does not share its perineurium with any other inners; more
accurate representation requires segmentation of the “outers” as well.
The user is required to set the “NerveMode”
in Sample (“nerve”) to
communicate the contents of the segmented histology files (S7 and S8 Text). The outer
nerve boundary, if present, is defined with a separate mask (n.tif
). In
the case of a compound nerve with epineurium, the pipeline expects the
outer boundary of the epineurium to be provided as the “nerve”. In the
case of a nerve with a single fascicle, no nerve mask is required—in
which case either the outer perineurium boundary (if present) or the
inner perineurium boundary (otherwise) is used as the nerve
boundary—although one may be provided if epineurium or other tissue
that would be within the cuff is present in the sample histology.
Lastly, an “orientation” mask (a.tif
) can be optionally defined. This
mask should be all black except for a small portion that is white,
representing the position to which the cuff must be rotated. The angle
is measured relative to the centroid of the nerve/singular fascicle,
so this image should be constructed while referencing n.tif
(or, if
monofascicular, i.tif
, o.tif
, or c.tif
). By default, the 0º position of
our cuffs correspond with the coordinate halfway along the arc length of
the cuff inner diameter (i.e., the cuff will be rotated such that the sample center, cuff
contact center, and centroid of the white portion of a.tif
form a line) while the
circular portion of a cuff’s diameter is centered at the origin (Note: this rotation process uses “angle_to_contacts_deg”
and "fixed_point"
in a “preset”
cuff’s JSON file, see S17 and S19 Text). If a.tif
is provided, other cuff rotation methods
(“cuff_shift”
in Model, which calculate “pos_ang”
) are
overridden.
The user must provide segmented image morphology files, either from
histology or the mock_morphology_generator.py
script, with a specific
naming convention in the input/
directory.
Raw RGB image, to be available for convenience and used for data visualization:
r.tif
(optional).Combined (i.e., inners and outers):
c.tif
.Inners:
i.tif
An “inner” is the internal boundary of the perineurium that forms the boundary between the perineurium and the endoneurium.
Outers:
o.tif
An “outer” is the external boundary of the perineurium that forms the boundary between the perineurium and the epineurium or extraneural medium.
Scale bar:
s.tif
(scale bar oriented horizontally, required unless scale input mode is set to ratio).Nerve:
n.tif
(optional for monofascicular nerves).Orientation:
a.tif
(optional).
For an example of input files, see Fig 2. The user must properly set
the “MaskInputMode”
in Sample (“mask_input”
) for their provided
segmented image morphology files (S7 and S8 Text).