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Automated calculation of the cell's membrane curvature radius

The Find-Curve macro for the ImageJ program (Schneider et al. 2012) automatically processes all cell stacks contained in a root folder indicated by the user.

Recommendations

Avoid file paths containing spaces. Depending on your OS and ImageJ version this kind of paths can be non compatible with certain open/save functions.

As initially designed, the macro is configure to find black shapes within a white background.

Brief description

For each file, the program performs the following steps:

  1. Identification of the slice with the largest area.
Original Identified biggest slice
Original image (3D representation) Identified "Best" Slice
  1. On this slice the angle (OA, OB) is calculated for every point (O) of the perimeter, with A and B two neighbors points respectively upstream and downstream to O.
Segments identification
Angle values along the cell perimeter
  1. The identification of local maximal angle values along the perimeter allows to delimit segments and draw the regular polygon model for the cell. The concave or convex property of the segments is determined using the regular polygon as reference.
Regular Polygon and summits
Identified summits (white circles)
Regular fiiting polygon (grey shape).
Convex segments (blue letters).
  1. For all segments, the radius of the best fitting osculating circle is calculated (Mesmoudi et al. 2010, Berutti et al. 2012). This value is the curvature radius R of the studied segment.
osculating circle calculated Radius of curvature
Principle of the Osculating circle. Application to the determination
of the curvature radius
of segment B. The fitting osculating
circle is represented.
  1. A .html report file is automatically generated.

Options

Options

The user has the possibility to choose between automatic and manual identification of the best slice.

Moreover the analysis can be performed in the three (X, Y, Z) dimensions.

Test set of stacks acquisitions

If you want to test this program, we provide you a set of several stacks:

Download here

Contributors

LBMC Logo CNRS Logo ENS Logo
CLUET David [email protected]
VERGIER Blandine [email protected]

License

Copyright CNRS 2013

This software is a computer program whose purpose is to automatically identify segments of the cytoplasmic membrane and calculate their radius of curvature.

This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL: http://www.cecill.info/index.en.html

As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author,the holder of the economic rights, and the successive licensors have only limited liability.

In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security.

The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms.

Requirements

The FIND_CURVE macro requires ImageJ v1.49g or higher (Download).

For ImageJ, the conversion of the analyzed stacks into animated GIFs requires the (Gif-Stack-Writer Plugin).

Files

  • [] src
    • README.md
    • LICENSE
    • Installation.ijm
    • Installation_FIJI.ijm
    • [] doc
      • 3D.jpg
      • Avatar.jpg
      • FIJI.jpg
      • Identification.jpg
      • IJ.jpg
      • Logo_cnrs.jpg
      • Logo_ens.jpg
      • Logo_LBMC.jpg
      • Osculating_circle.jpg
      • Segment.jpg
      • Slice.jpg
    • [] macro
      • CleanMemory.java
      • CloseImage.java
      • CNRS.jpg
      • ENS.jpg
      • Explorer.java
      • Find_Curve.java
      • HTML_Curve.html
      • LBMC.jpg
      • macro_AboutPlugin.java
      • Main.java
      • ROIeraser.java
      • Startup_CL.txt
      • style_Curve.css
      • tableline.html
      • Trigo.tif
      • UCBL.jpg

Installation

The FIND-CURVE macro can be automatically installed with all required files in ImageJ and FIJI. Please follow the specific instructions described below.

ImageJ Logo

  1. Open ImageJ.
  2. Open the src folder of the FIND-CURVE macro.
  3. Drag the Installation.ijm file on ImageJ Menu bar to open it.
  4. In the Menu bar of the macro select the Macros/Run Macro option.
  5. The window will be closed automatically and all required files will be installed in the ImageJ/macros/Find-Curve folder. The shortcut Plugins/Macros/FIND-CURVE will be added in the Menu bar.
  6. Restart ImageJ to refresh the Menu bar.

FIJI Logo

  1. Open FIJI.
  2. Open the src folder of the FIND-CURVE macro.
  3. Drag the Installation_Fiji.ijm file on FIJI Menu bar to open it.
  4. In the console select the Run option.
  5. All required files will be installed in the Fiji.app/macros/Find-Curve folder. The shortcut Plugins/Macros/FIND-CURVE will be added in the Menu bar.
  6. Restart FIJI to refresh the Menu bar.

Update

Follow the same instructions as for the installation process.