Search found 25 matches

by votti
Tue Jan 07, 2020 3:52 pm
Forum: Data analysis
Topic: Creating ome.tiffs from .mcd via Jupyter Notebook
Replies: 1
Views: 1009

Re: Creating ome.tiffs from .mcd via Jupyter Notebook

Hi MalteLehmann,

Sorry I am seeing this only now!

The issue is that the metal format needs to be: (Metal)(Mass), e.g. Ir191, Yb171 etc. not '143Nd'.
I rewrote the documentation to make this more obvious.

Does this fix your problem?

Cheers, Vito
by votti
Sat Sep 07, 2019 8:15 am
Forum: Data analysis
Topic: IMC data transformation and normalisation across ROI
Replies: 2
Views: 1870

Re: IMC data transformation and normalisation across ROI

Hi there, I find it difficult to give universal recommendations for these kind of questions, as they really depend on the data quality and the planned downstream analysis, which can have various assumptions on the data structure. Thus, different downstream analysis methods suggest different transfor...
by votti
Fri Aug 02, 2019 8:57 am
Forum: Data analysis
Topic: Merge ROIs from IMC
Replies: 2
Views: 1638

Re: Merge ROIs from IMC

Hi, The ablation coordinates required to do this can be found in the XML embedded in the `.mcd` file. This gets also extracted as easier parsable`.csv` files when converting `.mcd` files to folders containing `.ome.tiff`s using the `imctools` library. (`Convert zipped IMC acquisitions to input forma...
by votti
Fri Aug 02, 2019 8:45 am
Forum: Reagents
Topic: Compensation slide
Replies: 6
Views: 4322

Re: Compensation slide

@Fluidigm stock concentrations: We just back-calculated the concentrations of the stock lanthanides from the antibody conjugation protocol, where Fluidigm writes that the stock solution should be diluted 5ul in 95ul Buffer to get to a 2.5mM final concentration -> 1:20 dilution -> stock has 50mM @Pip...
by votti
Tue Nov 13, 2018 8:35 am
Forum: Data analysis
Topic: Compensation slide acquisition
Replies: 3
Views: 3388

Re: Compensation slide acquisition

Hi, I think my suggestion form the protocol (https://docs.google.com/document/d/195eViUqHoYRKrkoy_NkIdJPmyx1-OuDaSjiWQBy4weA/edit?usp=sharing) is still the one I would recommend: 2. Load the slide and generate panoramas It can be easier to generate 1 panorama per row of the spillover array. These pa...
by votti
Wed Oct 31, 2018 4:59 pm
Forum: Data analysis
Topic: Rphenograph
Replies: 2
Views: 2493

Re: Rphenograph

Hi there, I remember comparing the two packages, Python and Rphenograph, some time ago and found no major difference between them. To my understanding, the implementation is 'simple' in the sense of 'easy to read code', Usually, the non-deterministic part of `phenograph` is the `Louvain method`, a g...
by votti
Mon Oct 08, 2018 4:26 pm
Forum: Data analysis
Topic: Checking uncertainty in Ilastik
Replies: 1
Views: 1575

Re: Checking uncertainty in Ilastik

Hi, One way is to export the uncertainties as images and using your image quantification tool of choice (eg CellProfiler or Ilastik) to quantify the total uncertainty of your images/over all images (eg MeasureImageIntensity using CP and exporting the image table as csv) . If you track how this chang...
by votti
Tue Aug 07, 2018 8:59 am
Forum: Data analysis
Topic: ome2singletiff error on windows, histocat conversion errors
Replies: 1
Views: 1451

Re: ome2singletiff error on windows, histocat conversion errors

Hi there,

I refer to our discussion on Github: https://github.com/BodenmillerGroup/imctools/issues/27
Short summary: The error was already recognized in fixed in the development version that can be installed via:

Code: Select all

pip install git+https://github.com/BodenmillerGroup/imctools.git@development
by votti
Fri Jul 20, 2018 11:03 am
Forum: Data analysis
Topic: Imctools
Replies: 15
Views: 9562

Re: Imctools

Hi Vito, Thank for that, I got it working. Yes, Raul's comments clarified some things about histocat++. Does "old_example_preprocessing_pipeline.ipynb" contain all steps from start to finish of the pipeline? Sorry for many beginner questions. Thanks, Santhosh Hi Santhosh, No problem, I recognize th...
by votti
Wed Jul 18, 2018 8:36 am
Forum: Data analysis
Topic: Imctools
Replies: 15
Views: 9562

Re: Imctools

Hi Vito, I am a beginner with Python and IMCtools, just a couple of questions: 1) Is IMCtools package supposed to be 'installed' via terminal or Jupyter notebook? Or am I supposed to copy it somewhere and call it? Sorry if terminology I'm using is wrong 2) is there a way to use histocat++ in this p...