Cardinal MSI Help

1–30 of 271

Welcome to the help group for Cardinal, an R toolbox for statistical analysis of mass spectrometry imaging experiments.

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Cardinal MSI Help, kbemis2

Sep 11

IMPORTANT UPDATE: We are migrating to Slack!

Update invitation links can be found by replying to this Github issue: https://github.com/kuwisdelu/

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IMPORTANT UPDATE: We are migrating to Slack!

Update invitation links can be found by replying to this Github issue: https://github.com/kuwisdelu/

Sep 11

Shuo Qian, kbemis5

Aug 29

Combine two MSImagingArrays for further peak alignment

Hi Kylie, I will try what you mentioned, and thanks for your explanation. Best, Shuo 在2024年8月29日星期四

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Combine two MSImagingArrays for further peak alignment

Hi Kylie, I will try what you mentioned, and thanks for your explanation. Best, Shuo 在2024年8月29日星期四

Aug 29

Marco Fidaleo, kbemis2

Aug 29

Different results with spectra and summarizeFeatures

Considering we are talking about (1) an average of intensities versus (2) a distribution of

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Different results with spectra and summarizeFeatures

Considering we are talking about (1) an average of intensities versus (2) a distribution of

Aug 29

Raven Buckman, kbemis5

Aug 9

Segmentation Error After Sub-Setting Pixels

Thanks so much! On Friday, August 9, 2024 at 12:27:53 PM UTC-5 kbemis wrote: Thanks! The error seems

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Segmentation Error After Sub-Setting Pixels

Thanks so much! On Friday, August 9, 2024 at 12:27:53 PM UTC-5 kbemis wrote: Thanks! The error seems

Aug 9

Orotomah Ameh Great, kbemis2

Aug 9

Export image metadata

It sounds like you are trying to export the image data itself, not metadata. Slicing an image as an

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Export image metadata

It sounds like you are trying to export the image data itself, not metadata. Slicing an image as an

Aug 9

aali...@gmail.com, … kbemis6

Jul 30

A couple questions re version 3.6 files and plotting

Hi Matt, It does not support writing multiple intensity channels currently. I am not sure that imzML

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A couple questions re version 3.6 files and plotting

Hi Matt, It does not support writing multiple intensity channels currently. I am not sure that imzML

Jul 30

jennifer.n...@gmail.com, … kbemis10

Jul 29

Exporting Data While Maintaining Clusters

Do you mean plotting the ion image shows a different scale of intensities compared to the mean

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Exporting Data While Maintaining Clusters

Do you mean plotting the ion image shows a different scale of intensities compared to the mean

Jul 29

Даниил Соболев

Jul 24

Unavailability of the mz removal in new version.

Dear Dr. Kylie Ariel Bemis, Recently, I tried to remove certain mz values from my dataset. However,

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Unavailability of the mz removal in new version.

Dear Dr. Kylie Ariel Bemis, Recently, I tried to remove certain mz values from my dataset. However,

Jul 24

Даниил Соболев, kbemis2

Jul 13

Plotting Different Smoothing Algorithms

The issue seems to be the processed plot is ignoring the dataset's pixel names. I am working on a

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Plotting Different Smoothing Algorithms

The issue seems to be the processed plot is ignoring the dataset's pixel names. I am working on a

Jul 13

Matthew Smith, kbemis3

Jun 28

Visualise ROI masks in v3.6

Perfect, that has resolved it. Thanks :) On Thursday, June 27, 2024 at 8:10:37 PM UTC+2 kbemis wrote:

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Visualise ROI masks in v3.6

Perfect, that has resolved it. Thanks :) On Thursday, June 27, 2024 at 8:10:37 PM UTC+2 kbemis wrote:

Jun 28

Ayush Praveen, kbemis2

Jun 10

sgmixn issue while running SpatialDGMM

This is fixed now. May take a couple days to appear on Bioconductor. If you need a fix sooner and

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sgmixn issue while running SpatialDGMM

This is fixed now. May take a couple days to appear on Bioconductor. If you need a fix sooner and

Jun 10

Marco Fidaleo, Jason Rodencal2

Jun 6

Identification of m/z differences in 2 different ROI

Hello! You can select ROIs in cardinal datasets in Cardinal v3.6. Then, it is fairly simple to assign

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Identification of m/z differences in 2 different ROI

Hello! You can select ROIs in cardinal datasets in Cardinal v3.6. Then, it is fairly simple to assign

Jun 6

Jason Rodencal2

Jun 5

Converting RDS to cardinal object

I managed to figure out conversion of the .RDS to Cardinal using this very helpful video posted

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Converting RDS to cardinal object

I managed to figure out conversion of the .RDS to Cardinal using this very helpful video posted

Jun 5

Marco Fidaleo, … Matthew Smith3

May 17

How to use .mzML files or to convert them into .imzML and .ibd

Hello, I too ran into this problem with targeted MSI analysis with Waters. As a temporary fix until

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How to use .mzML files or to convert them into .imzML and .ibd

Hello, I too ran into this problem with targeted MSI analysis with Waters. As a temporary fix until

May 17

May Institute NEU, kbemis2

May 16

Cardinal short course session in May Institute 2024 at Northeastern University

Thank you, Sai! -Kylie On Thursday, May 16, 2024 at 3:32:52 PM UTC-6 mayinsti...@gmail.com wrote:

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Cardinal short course session in May Institute 2024 at Northeastern University

Thank you, Sai! -Kylie On Thursday, May 16, 2024 at 3:32:52 PM UTC-6 mayinsti...@gmail.com wrote:

May 16

Marco Fidaleo, … kbemis13

May 7

Errore in get_matter_list_sublist(x, i, j) : failed to read data elements

Yes, the imzML offsets are telling Cardinal to load spectra that don't exist in the ibd file, so

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Errore in get_matter_list_sublist(x, i, j) : failed to read data elements

Yes, the imzML offsets are telling Cardinal to load spectra that don't exist in the ibd file, so

May 7

Marco Fidaleo, kbemis11

May 4

Cardinal Version 3.6

Thanks Kylie, very clear, as usual! Best, M Il giorno sabato 4 maggio 2024 alle 19:04:58 UTC+2 kbemis

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Cardinal Version 3.6

Thanks Kylie, very clear, as usual! Best, M Il giorno sabato 4 maggio 2024 alle 19:04:58 UTC+2 kbemis

May 4

Marco Fidaleo, kbemis2

May 2

How to focus on a specific class of molecules

You are using s=0, so there is no sparsity enforced, so all clusters will be informed by all ions.

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How to focus on a specific class of molecules

You are using s=0, so there is no sparsity enforced, so all clusters will be informed by all ions.

May 2

Apr 30

Cardinal 3.6 -- major update with breaking changes

Dear all, Cardinal 3.6 should be released tomorrow. This is a major update with some breaking changes

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Cardinal 3.6 -- major update with breaking changes

Dear all, Cardinal 3.6 should be released tomorrow. This is a major update with some breaking changes

Apr 30

Marina Zavolskova, kbemis2

Apr 30

Not directly without some additional calculations. One way I can think of would be to use the

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Not directly without some additional calculations. One way I can think of would be to use the

Apr 30

yonghu...@gmail.com, kbemis2

Apr 10

How to combine multiple MSI datasets acquired in centroid mode?

It isn't exactly a bug. It is because if centroided peaks are stored in "processed"

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How to combine multiple MSI datasets acquired in centroid mode?

It isn't exactly a bug. It is because if centroided peaks are stored in "processed"

Apr 10

Apr 1

a possible bug in `subset` function

Dear Cardinal developers, I hope this message finds you well. I am writing to bring to your attention

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a possible bug in `subset` function

Dear Cardinal developers, I hope this message finds you well. I am writing to bring to your attention

Apr 1

Mar 22

Failure to plot high resolution images

Hello, Love using this package, such flexibility and functionality. I have started to encounter a

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Failure to plot high resolution images

Hello, Love using this package, such flexibility and functionality. I have started to encounter a

Mar 22

yonghu...@gmail.com, kbemis2

Mar 12

Release of ShinyCardinal, a GUI version of Cardinal

Cool! -Kylie On Tuesday, March 12, 2024 at 11:33:57 AM UTC-4 yonghu...@gmail.com wrote: Dear Cardinal

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Release of ShinyCardinal, a GUI version of Cardinal

Cool! -Kylie On Tuesday, March 12, 2024 at 11:33:57 AM UTC-4 yonghu...@gmail.com wrote: Dear Cardinal

Mar 12

marco.gi...@gmail.com, … kbemis6

Mar 11

removing matrix regions from dataset

Thanks for bringing this one to my attention with an example. It took a little investigating, but a

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removing matrix regions from dataset

Thanks for bringing this one to my attention with an example. It took a little investigating, but a

Mar 11

Davide G. Franchina, … Marco Fidaleo9

Mar 10

image(ssc) returns no image

Thank you, Kylie! It worked perfectly! Cheers, M Il giorno domenica 10 marzo 2024 alle 17:48:23 UTC+1

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image(ssc) returns no image

Thank you, Kylie! It worked perfectly! Cheers, M Il giorno domenica 10 marzo 2024 alle 17:48:23 UTC+1

Mar 10

pips...@gmail.com, … Jimmy Muldoon5

Mar 9

fatal error: fftw3.h: No such file or directory

Hi all Had a similar issue, Cardinal installation failing on linux with cc -I"/usr/share/R/

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fatal error: fftw3.h: No such file or directory

Hi all Had a similar issue, Cardinal installation failing on linux with cc -I"/usr/share/R/

Mar 9

cindy, Giulia Ricciardi4

Feb 23

Error when loading my data

Hello! I'm not sure about what could be the issue here. Maybe you can try to convert your data

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Error when loading my data

Hello! I'm not sure about what could be the issue here. Maybe you can try to convert your data

Feb 23

Davide G. Franchina

Feb 19

cannot create MSImagingExperiment()

Hi all, I am trying to create an MSImagingExperiment from scratch but I get this error: object <-

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cannot create MSImagingExperiment()

Hi all, I am trying to create an MSImagingExperiment from scratch but I get this error: object <-

Feb 19

Feb 12

coregistration of optical images

Hi, has the co-registration for the optical images been implemented yet? I am looking for a way to

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coregistration of optical images

Hi, has the co-registration for the optical images been implemented yet? I am looking for a way to

Feb 12

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