memory problems-TissueView

[Kimberly Nelson]

I know that TissueView/BioMap functions are limited by RAM availability, but is there any other factor limiting function? Virtual memory perhaps? other types/sources of computer memory??

For example, I get different “errors in function”, such as “TISSUEVIEW_EVENT” or “PBMT_COPYSCANTOWINDOW” which follows with the message “Unable to allocate memory: to make array”.

This is strange, considering I have 4 GB RAM on this computer. What sort of MB or GB file limits exist in BioMap? TissueView?

Have others on this site figured out a magical size of file at which you should aim to collect so that you can actually process in BioMap/TissueView?

Any help would be great. Thank you in advance. :cheer:

[b]Update: I would like to add that I have 4 GB RAM and over 30 GB free space on this computer[/b].

[Dodge Baluya]

Could you give more details on what you are trying to do? There are some programming errors in Biomap which can be avoided if you follow a specific step.
Also working on a 64bit OS environment would give you more accessible RAM. Hope this helps.

Dodge

[Kimberly Nelson]

Specifically, I was trying to baseline correct the entire image, and normalize the image, which creates an output image to a new window. I can successfully do both of these functions with very small images, and if I don’t have anything else open in the windows. But when I have multiple images open, it seems the memory gets used up and no other functions are possible. I was just wondering if a specific limit exists?
Unfortunately I don’t have access to a better computer. B)

[Dodge Baluya]

Hm. I don’t think there is a specific limit in the software, as I was dealing with the same issues as you have until I upgraded the computer with (Win7) 64bit OS and 16GB ram. 32bit OS have a 3Gb access limit. Try matching your swap page (virtual ram) with your physical ram and see if that helps.

There is also a bug when you are working on the LAST pane (say if you have a 2×2 layout you are trying to do a function on the image on the 4th pane) it crashes because it automatically tries to look for the next pane before you can execute the command.

[Kimberly Nelson]

Thank you very much, I will see if I can work on the computer upgrade in the future.

[Markus Stoeckli]

[b]knelson wrote:[/b]
[quote]Specifically, I was trying to baseline correct the entire image, and normalize the image, which creates an output image to a new window.[/quote]
Typically we would do in my lab normalizations and BC on extracted images, not the full data set. This is much faster and does not require a significant amout of memory.

[Kimberly Nelson]

Hello again…UPDATE: I now have a 64-bit Win 7 unit for TissueView. Do you have any install advice? Words of wisdom? The folks at AB SCIEX haven’t officially tested it on a Win7 system, so if we have install problems (it looks like we may), we won’t exactly have a “how to” pdf available. Thank you in advance for any help you can provide!
-Kimberly

[Dodge Baluya]

Not much to add to. I would advise you to install on a directory with no spaces or starting with numbers. For some reason I get data errors in BioMAP data directories(random not all the time) whenever those are present. Maybe in TissueView they fixed it already or they dont use it at all.

[Markus Stoeckli]

There are no known issues with Windows 7 32 or 64 bit. As knelson pointed out, BioMap is somewhat picky about the directory names. Best to stay with the basics, no special characters. And should you run into an issue, please report it back here on this forum.

Markus

[Author]

Posts