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saeyslab / DeepLearning_for_ImagingFlowCytometry

A framework around Tensorflow-Keras that makes it easy to train and evaluate any deep learning architecture on imaging flow cytometry data.
GNU General Public License v3.0
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paper #4

Open aliechoes opened 4 years ago

aliechoes commented 4 years ago

Hi

For which paper this package is developed?

MaximLippeveld commented 4 years ago

Hi, this for the paper Classification of Human White Blood Cells Using Machine Learning for Stain‐Free Imaging Flow Cytometry. Thanks for your interest!

aliechoes commented 4 years ago

thanks for the reply. I actually found your paper quite interesting. I am also working on IFC as well. so it was a quite good to see your work. cheers

aliechoes commented 3 years ago

Thanks again for the reply. I found the paper quite interesting. I am wondering whether the data is publicly available for experiments?

MaximLippeveld commented 3 years ago

Hi, glad you liked it! The data is available. This directory contains everything used in the paper.

aliechoes commented 3 years ago

awesome! thanks :)

aliechoes commented 3 years ago

Hi Maxim, So I download the files and try to use cifconvert. However it seemed quite challenging to convert the files. Also, I was not able to open the .daf files using IDEAS. Not sure what was the problem. I am wondering if the hdf5 or .tif files are somewhere stored which I can use directly? in addition, can you please specificy which channels are used? Thanks a lot!

MaximLippeveld commented 3 years ago

Indeed, cifconvert isn't bug free, unfortunately :-) It should work in most caes, though. What problems did you run into?

What version of IDEAS are you using to open the daf files?

I don't have the hdf5 files available, currently. Can you open the cifs in IDEAS? Then you can export the tif files, maybe.

aliechoes commented 3 years ago

I am using IDEAS 6.2. It tells that there is something wrong with the .daf files though. I could however open the .cif file alone. but I was not sure if all the cells in the .cif files are the one used in your work. For example, I was not sure whether focused cells were gated or not.

MaximLippeveld commented 3 years ago

I indeed used only single, focused cells. Have you tried re-downloading the .daf files? I will try later today whether I can still open them.