Use this plug-in for Image J (1.33 or later) to create z-projected (single plane) TIFF files for each channel from single- or multi-plane Olympus OIB or TIFF files. This plug-in will do this for every Olympus OIB/TIFF file in a directory (batch process). It will perform a max intensity z-projection on each channel (red, green, blue, etc) and then save as TIFF files. Simply right click to "Save Link As" and then place the macro in the macro folder within the Image J directory.

This macro requires installation of the BioFormats plug-in from LOCI at the University of Wisconsin (see below).

Splits an imagej stack into multiple substacks. The number of such substacks is user specified. Each substack may contain only a single image. This is a duplicate of the SplitStack plugin that is part of the UCSD Confocal Microscopy Plugins package.

Copy Stack_Splitter.class to the plugins folder and restart ImageJ.

This file will describe the procedures for anesthetizing small animals using isoflurane for the Xenogen and Maestro imaging workstations.

With this set of ImageJ plugins you will now have the ability to open and save Biorad .PIC format images. Download the file and unpack the .zip file into your ImageJ plugin directory.

Procedure for using Fluoview 1000

Taken from the Olympus software download web site.

This software will be read the data captured by FV1000/FV500/FV300. Images saved with FV file format (OIF, OIB, FV Multi-Tiff) can be read.


ExportEthat is a function to save with the common file format (BITMAP, JPEG, PNG, TIFF etc.) is added and separated from the saving with FV file format.


Since this software is for reading, image capture, measurement, analysis, 3D function etc. can not be used by this software.


Requirements:
Operating System : Microsoft WindowsXP SP2(English recommended)
Available space in hard disk : 100MB or more (Sufficient space for secure installation.)
Display monitor: 1280X1024 pixel resolution with 32bit true colors or more
HT Technology must be disabled in BIOS setting.
Windows Automatic Updates and any Virus Protection program has to be disabled.
If you have already installed FV10-ASW in PC, this software cannot be installed.

For our users using the Olympus 1000 Fluoview. Please note that ImageJ is the BIPL recommended application to use when viewing images captured with the Fluoview 1000. There have been some issues with images not displaying properly and not being able to analyze images when using the FV-1000 viewer software.

The following was taken from OME at LOCI - Software - Bio-Formats library

Bio-Formats is a standalone Java library for reading and writing microscopy file formats, written by Melissa Linkert, Curtis Rueden, Chris Allan, Eric Kjellman and Brian Loranger. It is capable of parsing both pixels and metadata for a large number of formats, as well as writing to several formats.


Installation: Download loci_tools.jar, and drop it into your ImageJ/plugins folder. Next time you run ImageJ, a new LOCI submenu with several plugins will appear in the Plugins menu, including the Bio-Formats Importer and Bio-Formats Exporter.


ImageJ v1.37 and later automatically (via HandleExtraFileTypes) calls the Bio-Formats logic, if installed, as needed when a file is opened within ImageJ—e.g., when using File/Open instead of explicitly choosing "Bio-Formats Importer" from the Plugins/LOCI menu.


Upgrading: To upgrade, just overwrite the old loci_tools.jar with the new one. You may want to download the latest version of ImageJ first, to take advantage of new features and bugfixes.

This excel file will calculated the ideal iris diameter for an airy disk of 1, the nyquist sampling rates, and the backprojected pinhole radius for previously calculated airy disk diameter. All that needs to be entered is the magnification and numerical aperture (N.A.) of the objective, the excitation wavelength, and refractive index (R.I.) of the lens. It can also calculate the backprojected pinhole radius for other iris diameters. The Nyquist sampling rates are in NANOMETERS, convert them to microns for use in the Biorad software.

This information is only valid for a BIORAD machine.

The following attachments are the point spread functions for the Bio-Rad 1024 Multiphoton at the FTIC (488 nm) and Texas Red (568 nm) wavelengths using the 60x oil objective. A pdf is included that has the sampling information for the point spread functions.
This data is ONLY valid for the multiphoton.

Software for 3D analysis of confocal images. Version has not changed since 1996, but still runs well on most Windows platforms. Download version 4.2 (Windows 3.1, 95/98/NT/2000, 1.09 Mb)