[Markus Stoeckli]

Version 3.0 is also supported (different software).

markus

[Markus Stoeckli]

BioMap allows co-registration of data which is an extremely powerful feature for evaluation of data from different sources. Using this method, images from different animals may be compared, ROIs can be transferred between data sets and different modalities.

The easiest way to achieve co-registration between MSI and optical data is modification of the header. Let me give an example: Am MSI was acquired with a raster of 0.1 mm, resulting in 200 x 100 data points. An optical image of the same section was taken at a higher resolution, resulting in an image with 1000 x 500 points. Both files are loaded in BioMap and lets assume that both images have a voxel size of 1 x 1 (depending on the image acquisition version, this might also be the actual dimension, in our case 0.1). Activate the windows with optical image and select Edit – Header from the menu. Switch to the Coregistration tab and enter 0.2 in the scaling field for x and y (0.02 if the MSI voxel size of the MSI is 0.1). Press Done and the image is co-registered with the MSI. Copy it as overlay to the MSI to see the effect of the method. Once the image is co-registered, save it to the Scan+ database where it will retain its parameters.

markus

[Markus Stoeckli]

We have BioMap running under Linux on a dual-processor workstation and it works well with data from the 4700. The mayor bottleneck we found is RAM size and disk access speed.

markus

[Markus Stoeckli]

This is simple (but might be expensive). You need twice the amount of RAM of your image size.

markus

[Markus Stoeckli]

*.t2d and *.set files are mass spectra and settings files generated by the 4700 Explorer software from Applied Biosystems. They can be opened with ‘Data Explorer’ from the same company.

markus

[Markus Stoeckli]

We’ll look into it as soon as we get the ILD VM for MAC. The RSI site really sucks – after numerous unsuccessful tries in downloading the software we gave up… 🙁 and ordered a CD. Let’s see.., should we get the software, we’ll install it on a G5 and test it with BioMap.

markus

[Markus Stoeckli]

No, things are not that simple 😕 . This is all about physics and the properties of a time-of-flight analyzer. The flight time is in a first order approximation proportional to the square root of the mass-to-charge ratio of the flying particle. Since we use a digitizer with a fixed time raster for data acquisition, we end up with data points in the time axis and not in the m/z axis. Most instrument manufacturers use a high order (typ. n > 4) polynomes for time into mass calculation. Since we have not access to most of these calibration equations, we work with a calibration table to our image files (named *.t2m). All the image points are calibrated using this same table. If you load an image in BioMap and a calibration file is present in the same directory, the calibration file is used to label the x-axis. Otherwise, the x-axis is labeled with the volume number.

[Markus Stoeckli]

Could you give us more details? Does IDL RT 6.1 start OK? Do you get that error when you load BioMap or when you try to open an MSI file?

markus

[Markus Stoeckli]

This error was not heard of before 🙁 .

In the software MMSIT, the sample information is stored in a simple MS Access DB. My first guess is, that either your DB got modified or that the shared component for DB interfacing (MDAC) was modified to a different version.

In a first step, try to run the software with the default DB as it came with the installtion. If that does not help, check on the installation of MDAC on your computer. Use the ‘MDAC Component Checker’ from the MS site [url]http://www.microsoft.com/downloads/details.aspx?familyid=8f0a8df6-4a21-4b43-bf53-14332ef092c9&displaylang=en[/url] to get the relevant information. I just tried it with MDAC 2.7 SP 1 and it works fine. If you have an older version, try upgrading to the most recent one ([url]http://msdn.microsoft.com/data/Default.aspx[/url]). Please report on your Windows version, service packs and MDAC version should the error persist.

Hope this helps,

markus

[Markus Stoeckli]

I was thinking about a training session during the ASMS conference in St. Antonio? Any interest?

markus

[Markus Stoeckli]

I can only estimate the flow rate of of our spray since we use a TLC sprayer operated by Bernoulli’s principle. We ajdust the spray to form a fine mist setting the pressure to approx 0.8 bar. This results in an estimated flow of 1 ml/min. We spray 8 ml in 30 minutes, with cycles of 10 s spray and 30 s pause.

Markus

[Markus Stoeckli]

Yes, it works. We use it in our lab and it’s relatively robust and reproducible. In a typical coating we spray 8 ml of saturated CHCA solution in 50:50 ACN/0.1%TFA using a TLC sprayer. The authors state:[quote] The sample is allowed to dry for 1-2 min before the next coating cycle[/quote]
IMHO it is a requirement to never let the sample completely dry in between spray cycles ❗ .

Markus

[Markus Stoeckli]

The provided license enables MSI functions but not MRI specific tools. Most people downloading the software from this site will use it with MSI data and not for MRI data processing.

There’s nothing wrong with your installation, what you observe is by design…

markus

[Markus Stoeckli]

I completely agree with you and corrected my previous post. That’s how it should be:

[b]*.img:[/b] 16-bit signed integers

[b]*.t2m:[/b] 32-bit floats

[Markus Stoeckli]

I verified the locations as indicated in the structure and it ckeckes out fine. You may use a hex editor to validate that your file was written correctly. The absolute locations are:

offset 42: D Points
offset 44: X Points
offset 46: Y Points

It might be an alignment problem with your compiler…

markus

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