ChiToolbox

MATLAB code for handling hyperspectral data generated by SIMS, FTIR and Raman instruments. @AlexHenderson00

[ChiToolbox @ChiToolbox]

Hello! Long time eh?
This is to let you know we've moved from Bitbucket to GitHub. Updates (by running ChiUpdate) will still return code from Bitbucket (with a warning). However, ongoing we recommend replacing the code with a new version from GitHub.
https://t.co/1a0BzPeExQ

[Alex Henderson 🇬🇧🇺🇦 bsky: @alexhenderson.info @AlexHenderson00]

New release of #python code to read hyperspectral image files produced by @Agilent #FTIR spectrometers.
- Reads *.seq and *.dmt files.
- Finds files in subfolders.
- Extract numpy arrays and metadata.
- Exports to @HDF5 format.
https://t.co/fTywcQqb60

#infrared #opensource

[ChiToolbox @ChiToolbox]

The mass spec peak detection facility now has the option of outputting all detected peaks, rather than the default of the 500 most intense.

peaks = mydata.peakdetect('numpeaks', -1);

You can visualise them too...

peaks = mydata.peakdetect('numpeaks', -1, 'vis');

[ChiToolbox @ChiToolbox]

Co-located plotting routines for easier customisation.
Tick marks now point out of the plot, to prevent confusion with spectral peaks. Especialy irritating with centroided mass spec plots.
What a PITA this was 😒

[ChiToolbox @ChiToolbox]

Changed spectral plot system so removed ranges are not drawn, rather than joined together
before=tissue.spectrumat(100,100);
after=before.removewax.removeco2;
subplot(3,1,1); before.plot('nofig');
subplot(3,1,2); after.plot('nofig','legacy');
subplot(3,1,3); after.plot('nofig');

[ChiToolbox @ChiToolbox]

Sigh...

[monkeyUser @ismonkeyuser]

Feature Complete (https://t.co/tk7z8xFm4y)

[ChiToolbox @ChiToolbox]

Already have ChiToolbox installed (using the Git method)?
Simply run
ChiUpdate
to bring your installation up-to-date

[ChiToolbox @ChiToolbox]

Added some validation methods: ChiHoldoutTest, ChiKFoldTest, ChiLOOCVTest, ChiBootstrapTest.

eg. 5-fold PCA on Raman spectra:
mydata = ChiRamanSpectralCollection(...);
result = ChiKFoldTest(mydata, 5, 'pca');
result.percentcorrectlyclassified

[ChiToolbox @ChiToolbox]

Impromptu presentation on ChiToolbox during lunch at the Chemometrics in Vibrational Spectroscopy webinar programme organised by the Raman Imaging Group in the Faculty of Chemistry, Jagiellonian University in Kraków.
https://t.co/3BA277VDNR

[ChiToolbox @ChiToolbox]

Data processed using ChiToolbox

[Alex Henderson 🇬🇧🇺🇦 bsky: @alexhenderson.info @AlexHenderson00]

My slidedeck from the Chemometrics in Vibrational Spectroscopy webinar, organised by the Raman Imaging Group @JagiellonskiUni, can be found here https://t.co/HksZfq7FuV
#chemometrics #datascience #infrared #raman

[ChiToolbox @ChiToolbox]

@arne_raulf @AlexHenderson00 @OfficialUoM @ruhrunibochum @clirspec @dfg_public https://t.co/V5YHrvCXd1

[ChiToolbox @ChiToolbox]

2020 Vision (Dubious Design Decisions) by @AlexHenderson00 #infrared #matlab https://t.co/WEhNuPhFnZ via @SlideShare #openvibspec

[ChiToolbox @ChiToolbox]

2020 Vision (Dubious Design Decisions) by @AlexHenderson00 #infrared #matlab https://t.co/WEhNuPhFnZ via @SlideShare #openvibspec

[ChiToolbox @ChiToolbox]

Updated kmeans (for images) to provide spectra relating to the centroids of the clusters.
im = ChiFile; % an image
k = 5; % number of clusters
c = im.kmeans(k);
https://t.co/hXoKmS0vem
c.centroids
for i = 1:k
c.centroid(i)
end

[ChiToolbox @ChiToolbox]

Improved tock() function (a drop-in replacement for MATLAB's toc function) to allow text to be prepended and/or appended
x = tic;
<do something>
tock(x, 'prepend', 'That took:', 'append', 'Wow!');

[ChiToolbox @ChiToolbox]

Added better datapoint tips for scores plots produced by PCA,CVA and PLS

[ChiToolbox @ChiToolbox]

Added partial least squares regression (PLS1)
(class membership needs to be numeric)
x = ChiFile;
c = ChiClassMembership('labels', [1,2,3,4,5]);
x.classmembership = c;
p = x.pls;
p.plotxscores(1,2)
p.plotweights(1)
p.plotcumexplainedvariance;

[ChiToolbox @ChiToolbox]

Added Savitzky-Golay smoothing

x = ChiFile;
window_length = 9;
s = x.smooth(window_length);

[ChiToolbox @ChiToolbox]

Sorry, not really been keeping up-to-date with updates 😶
Time you found out what we've been up to during lockdown 🔒

[ChiToolbox @ChiToolbox]

Excited to attend the kick-off meeting for OpenVibSpec, a new project to develop #opensource vibrational microspectroscopy software
We will present design decisions made while developing the ChiToolbox; some good, some less so :-/
https://t.co/eFy10xhrzH

https://t.co/eFy10xhrzH

[Arne Raulf @arne_raulf]

On Monday the #OpenSource hackathon on #spectroscopy will start. In Bochum we will find support by top-class colleagues from
@OfficialUoM @UniNMBU @ruhrunibochum @Leibniz_IPHT @clirspec @BhargavaGroup @BeckmanInst @CancerCenterIL
@nanbelarus
With support of #DFG! @dfg_public