[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.

[Dodge Baluya]

How often do you use “Mean with BC” instead of just “Mean” when extraction a particular m/z?

[Dodge Baluya]

Thanks, I already found the BC implementation in BioMap, described on the ‘usually ignored’ help (PDF) file.

[Dodge Baluya]

Hi Ramin,

I am guessing you use an extractor to convert the raw data into analyze format?
Most likely it is a conversion issue, which is converting the type of data (int) but not the data itself? A common problem in programming (pointer issues) that still haunts me till this day…

Hope this helps,

Dodge

[Dodge Baluya]

I also did some testing using dummy data (see excel to analyze topic by markus for more details) in img form. The displayed average in the ROI panel is correct.

[Dodge Baluya]

Let me get more details to help solve this problem, I’m concerned that if this is true then this needs to be addressed as soon as possible.
How do you average your raw data for the whole image (non-ROI method)?

Analysis -> Plot -> ROI should give you the average (intensities/pixel)

[Dodge Baluya]

Hi Ramin,

I believe the intensities are stored as single precision floats thus is not limited to 32767. (see the data structure, please correct me if I’m mistaken)
Think of the data points as containers for intensities values and the container are labelled with m/z. You can only work with a max of 32767 containers at one instance.

You have to be careful when comparing your raw data with the Highlighted ROI data as most of the time ROI data is averaged according to the area you specified and the raw data is not.

Hope this helps.

Dodge

[Dodge Baluya]

Thanks for this helpful code. I am actually interested to get some intensity data w/ position out of .img format to excel (or some other format) in order to do some data processing. Same concerns as the person who posted “Re:Export raw data from image”
This code would serve as a starting point.

[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.

[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

[Dodge Baluya]

You can use the Tissueview Manual to help you through some of the concepts in Biomap although some of the commands are not placed on the same location.

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