Vasco summer start #20
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Made a ton of changes!
Run PlotTest.m to make 3D flow-cytometry style plot. Needs a lot of work.
Added scrips to analyze data. still needs a lot of work
Made some major formatting changes! the places marked with "##" (just ctrl+F for ##) are notes on things that make good specific things to be working on, particularlyy for michale Also added feature to automatically save the exacdt file that was run everytime we run teh code. This should help with record keeping and everythnig a ton.
Simplified Gal8 Inputs and Outputs
Made some very big changes so I split it to a new Branch. The biggest change is the "m_DirectToBax_2" which is a file that hsould be much easier to put into a GUI now
New Plan is GUI1: Prep for Baxter GUI2: Baxter (goal is to get label matrix of cell labels so taht we can track over time) GUI3: BF_Analysis program to add Gal8, uptake, etc GUI4: Vasco makes analysis suite in R
All code from the new script is put into the GUI. The only thing left to do to get the GUI to run is to set up the ImageAnalyses cell array variable correctly. Also still need to change the layout of how the image planes are selected for each function.
…ding image planes. Started to mess with turning selections into struct data type
…/BaxterAlgorithms into SingleParticleIdea
Feeling really good about this version of the code! The only major modification left is to incorporate the single-well selection, and then incorporate it into the GUI. Marked potential long-term improvements with #PROJECT Updates: parfor loop fully functional Analyzes all Images and exports analysis Functions Made for cleaner, better code: BronkSegment LabelAnalysis CumCell
Analyzing a different experiment which exposed bug in the Img2 component and Gal8 part of BronkSegment. Would like to add single-cell level option soon. Just need to add a for loop within LabelAnalysis and probably the export and storage functions
Tiny Mistake
Cleaned up some text
Vasco, start with this to figure out how to structure the data so it's easiest to analyze and feed into your flowchart idea. The current StructOut Structure may not be optimal, Also later I'd like to add Kamerons Manders Coefficient code
Minor Updates and Edits
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