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" `_. + 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" `_. + 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" `_. + 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():