#  Software 

 



### **Microscope Setup Tutorials**

Use the [ZEISS Portal](https://urldefense.proofpoint.com/v2/url?u=https-3A__portal.zeiss.com_iqr-2Dacademy_video_Bqe5qUeMhiTf2Taot-5FL7xi&d=DwMFJg&c=WO-RGvefibhHBZq3fL85hQ&r=z_WX6LibTy--z3DCxbHRul0K_gTXsttWP1QL1_aIOk8&m=cXHx-dPpJXJVpe5dDL3rlcW-ZPlBv038x2bAt5yadAZDfa3j9Iiat-pJSH9_4shs&s=Ntnvp624A8pr6VfwvD6xl5_hGLu9oGeqGQA7fedoqvY&e=) to familiarize yourself with any microscope at HCBI and setting up its acquisition parameters.

### **ZEN**

For a free copy of **ZEN lite** image processing software, click here: [ZEN lite](https://portal.zeiss.com/download-center/softwares/mic) (Windows only). The HCBI recommends frequent downloads of ZEN to ensure your software is up-to-date and compatible with files from our newest microscopes.

For image analysis help, use: [Zen Blue Image Analysis Guide ](/file_url/210)PDF or the [Zen Portal Image Analysis Playlist](https://portal.zeiss.com/iqr-academy/video/BiAyEi4tEHEz4V6PxKSnxc)


### **Fiji/ImageJ**

For a free copy of **Fiji (ImageJ)** image processing software, click here: [Fiji](http://goo.gl/T7eKTP) (Windows or Mac)

Click [here](http://fiji.sc/Documentation) to be redirected to the extensive Fiji online documentation  
Click [here](http://rsb.info.nih.gov/ij/docs/) for a link to the ImageJ 1 documentation

### CellProfiler

CellProfiler[ Manual](https://cellprofiler-manual.s3.amazonaws.com/CellProfiler-4.2.8/index.html)

### **arivis Pro**

Click here for [arivis Cloud](https://www.apeer.com/app/)

Click here for an[ introduction to arivis Cloud](https://www.zeiss.com/microscopy/en/products/software/arivis-cloud-ai.html#accordionItem-1321530275)

Click here to view six 30-minute [introductory videos to the arivis Pro software.](https://www.zeiss.com/microscopy/en/resources/insights-hub/life-sciences/getting-started-with-zeiss-arivis-pro.html)  
Click here to read [several use case and case study documents.](http://zeiss.com/microscopy/en/resources/insights-hub.html?f_page=1&f_query=arivis)

### **IMARIS**

Click [here](http://www.bitplane.com/download/manuals/ReferenceManual6_1_0.pdf) to download the **IMARIS Reference Guide**.  
Click [here](http://www.bitplane.com/learning) to visit the **IMARIS Learning Center**



 

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 Attachments- [  picture\_as\_pdf  image\_analysis\_guide\_revised\_01-2014.pdf ](/sites/g/files/omnuum7436/files/hcbidoug/files/image_analysis_guide_revised_01-2014.pdf)
 
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