- IMAGEJ ND2 PLUGIN WINDOWS INSTALL
- IMAGEJ ND2 PLUGIN WINDOWS PLUS
- IMAGEJ ND2 PLUGIN WINDOWS SERIES
- IMAGEJ ND2 PLUGIN WINDOWS DOWNLOAD
IMAGEJ ND2 PLUGIN WINDOWS PLUS
The final SIPchart is composed of these five panels in false color, a resolution bar (histogram of FWHMs), five z-profile plots (at image center and four quadrant centers), plus a textual summary. The status bar shows the parameter that belongs to the current cursor position and panel. Each slice holds the corresponding parameters for all x-y positions. Results are stored in a "PanelStack" containing five 32-bit images (you can navigate between ISum, IMax, ZMax, FWHM, Skew). If the original image is not square, only the largest centered square will be evaluated.įrom each xy position, a z-profile will be analyzed: The prefix "binned-" will be added to the original image name. The program will performs the following actions:īefore creating the charts, the source stack is downscaled to x * y = 64 * 64 pixels using bilinear interpolation. (Please don't disturb the process with mouse clicks inside ImageJ windows). The SIPchart will be created within a few seconds. With the stack in front, choose tool menu Sip>Make SIPchart The clipboard could for example contain lines like below: Microscope=Zeiss IV Objective=63x NA=1.40 Excitation=488 Emission= 520 So you can re-use specifications from clipboard without re-typing. Optionally, choose menu Plugins>Macros>Add Microscope Specs from Clip If NA, Excitation and Emission wave lengths are entered, the program will draw the theoretical FWHM limit as red line into the resolution bar. Here you can to enter lens and instrument data - they will appear in the output plot. Optionally, choose menu Plugins>Macros>Set Microscope Specs in case your microscope uses different display conventions for left/right, back/front, up/down.Īnd make sure that voxel size is entered correctly, If necessary, choose Image>Transform> to flip horizontally, vertically, or Z.
IMAGEJ ND2 PLUGIN WINDOWS SERIES
If your z series is not organized as stack yet - choose menuįile > Import> Image Sequence in order to create a stack from individual images. 3: Live profile while dragging mouse across PanelStack Use your own image: 3)and show the through-Z plot for the corresponding x-y position.įig. When clicking and dragging the mouse inside "PanelStack", a live plot will be created (Fig. Select the Plot Live tool (" PL") from the tool bar and click on any of the colored panels, or inside window "PanelStack": SIPchart is built within seconds as shown in Fig.1. Note that tool menu Sip> Load Demo Stack From Web does not work anymore and will be removed in the next version.
IMAGEJ ND2 PLUGIN WINDOWS DOWNLOAD
IMAGEJ ND2 PLUGIN WINDOWS INSTALL
This documentation describes the SIPchart plugin running under ImageJ.īefore creating the first SIPchart from a 3D image (also called "stack"), it is necessary to install the ImageJ application (on Windows, OS X, or Linux) and to download the plugin "SIPchart_.jar". It is obtained by processing the 3D image of a thin fluorescent layer. SIPcharts SIPchart plugin for ImageJ Norbert VischerĪ SIPchart is suitable to quantify the sectioning quality of a confocal microscope.