Forum

Images go black when I access Image Composition dialog

2012-11-20T13:43:20Z

I am having a problem with the demo version of cyteseer. I am analysing data from a BD Pathway (Attovision) dataset which has been correctly collected and in which images are present. I can analyse the dataset from the main CyteSeer dialog box, and the analysis seems to run sucessfully (on Colocalization algorithm), and indeed when I go to View - Images, I can see the first image, albeit in the wrong colours. But then, when I try to alter settings in the Image Composition dialog, or if I try to load an image from another well, the image goes black and I cannot load any image at all, even the original one I started with.

Any ideas?

Thanks,
Sam

Installing CyteSeer x64 on Windows XP/Vista/7 - 64bit OS.

2009-12-10T21:36:09Z

Known Issues when Installing CyteSeer x64 Version on 64bit OS of Windows XP, Vista or 7.

Issue #1: When executing CyteSeer installation file, installation does not begin.
Issue #2: Error when installing into “Program Files” Directory
Issue #3: “Install VM Now” on JInstaller is Greyed Out. Option is not available.

Prior to Installation:

1. Install Java 64 bit directly from Java Website: http://www.java.com/en/download/manual.jsp
- Select the appropriate file for Java (64-bit), download and install. Fully complete installation before executing CyteSeer Installation File.

2. Right �Click� CyteSeer installation file. Select �Run as Administrator�. (Applies to Windows Vista and Windows 7 only)
- This allow CyteSeer installation file to have administrator permissions allowing installation to properly commence and access to the program files directory.

Trouble executing on linux?

2009-09-25T21:11:46Z

Just thought I push out a note that linux users may need to chmod +x the CyteSeer bin file to get it to execute.

problems in opening the program

2010-08-24T02:16:32Z

Hi,
I download the software (both the versions 2.7 and 2.0.14) but when I open it, the program doesn’t start…
I verify to have the last version of Java but it’s all right…
Can you please help me??
Thanks

Summary Statistic “Sum” of Mask Area not found…

2010-02-24T21:56:05Z

I noticed that the measurment list does not output the Summed (Capital Greek Sigma) mask area in a microtiter well, which also affects total integrated intensity measures. Can a �measure� plug-in be easily adapted to include this ouput, or, a new plug-in be created for this output? This is an important measure in the 3D cell cultures of the differentiation assays conducted here in the lab. It gives us an approximate measure the differentiation efficiency.

Thanks for the help,
PjB

Binary Mask to Labeled Mask to Masking the Gray Image

2010-02-22T23:37:07Z

Having some difficulty with simple thresholding and masking in pipeline environment. I create a simple binary mask via one of standard thresholding techniques. Debug mode shows this mask is generated. I then link this mask to a labeled mask, and debug mode shows that this mask is also created. I can apply the labeled mask to a gray image and this ouput is generated in debug mode. The problem is that these masks are not deposited into the results folder. The only mask ouput to the results folder is an archived “labeled mask” in ZIP format. Can you assist me by suggesting a proper course of action which will generate an image mask that can be used as the basis of pixel metrics? Thanks for your help, PjB

Installing CyteSeer on Ubuntu Linux

2010-02-09T01:22:24Z

Requirement when Installing CyteSeer on Ubuntu Linux.

Prior to Installation:
1. Install Java 32 or 64 bit from http://java.com/en

2. Install C++ library package “libstdc++5” or “libstdc++.so.5” for Ubuntu. Can use built-in “Synaptic Package Manager” or obtain from
Ubuntu package search site: http://packages.ubuntu.com/

3. Perform chmod a+x on Command Line to set permissions for CyteSeer install bin file before Installation: Example “chmod a+x CyteSeer_2_X_X_linux_i586.bin”

Detailed PDF for Ubuntu Installation available for Download: Click Here to Download Ubuntu Installation PDF

Installing CyteSeer 2.0.4 in Snow Leopard

2009-10-14T19:11:52Z

There is a known issue installing CyteSeer 2.0.4 in Snow Leopard. The work around is as follows:

- You have the change the order of the java virtual machine so that 32-bit is first.
- Utilities—> Java Preferences (bottom window) Java Applications—> drag 32-bit to the top.

There is a graphic attached demonstrating how to do this.

CyteSeer should always launch � with or without a license

2009-08-18T17:45:43Z

CyteSeer should always launch � with or without a license. A paid license is required to execute image processing functions but not to view images and data. There is an intermittent known issue where a dialog window will open at CyteSeer launch with the following text:

Sorry, your evaluation license for this software has expired

We are working on this issue but the simple work-around is to uninstall and reinstall CyteSeer. No data, licenses or settings will be lost on your machine.

Algorithms necessary to run analyses of beta-catenin in CyteSeer

2009-06-27T04:29:25Z

What algorithms would be necessary to run analyses of beta-catenin as indicated in “Monitoring Expression and Distribution of B-Catenin” section on your website (http://www.valasciences.com/articles/applications/monitoring-expression-and-distribution-of-catenin-z-05/). I’ve downloaded a trial version of CyteSeer software and would like to evaluate if it has applications for my interests.