Cell and Developmental Biology Microscopy Core

Free software for analyzing and processing image data

Fiji: ImageJ plus a large bundle of plugins, all packaged together in one easy-to-download application. Runs on Mac OS, Windows, and Linux. Very handy for new users who don't want to download individual plugins. Includes utilities for 3D viewing, video editing, measuring colocalization among others. Recommended for all CDB Micro Core users.

VLC: VLC media player is a free and cross-platform multimedia player that plays most multimedia files as well as DVDs, Audio CDs, VCDs, and various streaming protocols.  It's absolutely necessary for playing videos created using our Core's version of Arivis Vision4D at the Lightsheet workstation. 

CellProfiler: Free, open-source software from the Broad Institute for segmentation and quantitative analysis of microscope image data.

Ilastik: Free software that uses machine learning for interactive object recognition and segmentation.

ZEN Lite : Free software from Zeiss to open .czi files. Windows only.

LAS X Core: Free software from Leica to open images acquired on the Leica SP8 confocal or any microscope controlled by LAS X. Scroll down the linked page to find the version appropriate to your operating system. Windows only.

FileZilla Client: Recommended for SFTP transfer of files from the SOM Microscopy Core Server to your personal computer. Runs on PC or Mac. Instructions for using the server can be downloaded here*IMPORTANT* Do not use the Sourceforge installer on the main FileZilla Client download page, especially if you are using Windows. Adware and potentially unwanted programs (PUPs) will be installed along with FileZilla unless you are vigilant during the installation process. If you end up at the page showing the Sourceforge installer, click the link saying "Show additional download options" and select the desired version.

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