From c467470fc9cf8f030d612394557ac93c6d814c44 Mon Sep 17 00:00:00 2001
From: Richard Gerum <14153051+rgerum@users.noreply.github.com>
Date: Tue, 19 Dec 2023 11:08:10 -0500
Subject: [PATCH] mention integrations in index.rst
---
docs/source/index.rst | 39 +++++++++++++++++++++-
saenopy/gui/orientation/gui_orientation.py | 2 +-
2 files changed, 39 insertions(+), 2 deletions(-)
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 5f14a60..e6f5cc4 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -9,7 +9,8 @@ Welcome to the SAENOPY Documentation
SAENOPY is a free open source 3D traction force microscopy software. Its material model is especially well suited for
tissue-mimicking and typically highly non-linear biopolymer matrices such as collagen, fibrin, or Matrigel.
-It features a python package to use in scripts and an extensive graphical user interface.
+It features a python package to use in scripts and an extensive graphical user interface. The userinferface also has
+integrations for spheriods, fiber alignment and 2D traction force microscopy.
This migration immune cell demonstrated what scientific discoveries you can achieve with saenop:
@@ -57,6 +58,42 @@ Now you can start the user interface with:
``saenopy``
+Integrations
+------------
+
+Aside from saenopy's main use or 3D traction force microscopy we provide in our interface
+integrations to related methods to asses cellular forces.
+
+Spheroid
+~~~~~~~~
+3D traction force microscopy on multicellular aggregates (so-called spheroids).
+
+https://github.com/christophmark/jointforces
+
+* Mark C., Grundy T., Strissel P., Böhringer D., Grummel N., Gerum R., Steinwachs J., Hack C., Beckmann M., Eckstein M., Strick R., O'Neill G., Fabry B. (2020)
+ `"Collective forces of tumor spheroids in three-dimensional biopolymer networks" <https://doi.org/10.7554/eLife.51912>`_.
+ In eLife 9:e51912. doi.org/10.7554/eLife.51912
+
+Orientation
+~~~~~~~~~~~
+
+Use fiber alignment as a proxy for force if the material properties are not available.
+
+https://github.com/davidbhr/CompactionAnalyzer
+
+* Böhringer D., Bauer A., Moravec I., Bischof L., Kah D., Mark C., Grundy T.J., Görlach E., O’Neill G.M., Budday S. and Strissel P.L., 2023.
+ `"Fiber alignment in 3D collagen networks as a biophysical marker for cell contractility" <https://doi.org/10.1016/j.matbio.2023.11.004>`_.
+ Matrix Biology, 124, pp.39-48. doi.org/10.1016/j.matbio.2023.11.004
+
+pyTFM
+~~~~~
+Analyze force generation and stresses in cell colonies and confluent cell layers growing on a 2 dimensional surface.
+
+https://github.com/fabrylab/pyTFM
+
+* Bauer A., Prechová M., Fischer L., Thievessen I., Gregor M., & Fabry B. (2021).
+ `"pyTFM: A tool for traction force and monolayer stress microscopy" <https://doi.org/10.1371/journal.pcbi.1008364>`_.
+ PLoS computational biology, 17(6), e1008364. doi.org/10.1371/journal.pcbi.1008364
Citing Saenopy
--------------
diff --git a/saenopy/gui/orientation/gui_orientation.py b/saenopy/gui/orientation/gui_orientation.py
index f59603b..61c9cd3 100644
--- a/saenopy/gui/orientation/gui_orientation.py
+++ b/saenopy/gui/orientation/gui_orientation.py
@@ -202,7 +202,7 @@ def __init__(self, parent=None):
with QtShortCuts.QHBoxLayout():
self.edge = QtShortCuts.QInputString(None, "edge", "40", type=int, settings=settings, settings_key="orientation/edge", tooltip="How many pixels to cut at the edge of the image.")
QtWidgets.QLabel("px").addToLayout()
- self.max_dist = QtShortCuts.QInputString(None, "max_dist", "None", type=int, settings=settings, settings_key="orientation/max_dist", tooltip="Optional: specify the maximal distance around the cell center")
+ self.max_dist = QtShortCuts.QInputString(None, "max_dist", "None", type=int, settings=settings, settings_key="orientation/max_dist", tooltip="Optional: specify the maximal distance around the cell center", none_value=None)
QtWidgets.QLabel("px").addToLayout()
with QtShortCuts.QHBoxLayout():