Welcome to Mistic’s documentation!

Contents:

• 1. Introduction
  • 1.1. What is Mistic
  • 1.2. Motivation behind developing Mistic
  • 1.3. Mistic features
• 2. Functions
  • 2.1. get_cell_coords(pt,a)
  • 2.2. get_neighbours(coords,nx,ny,cells)
  • 2.3. point_valid(pt,a,nx,ny,cells,samples,r)
  • 2.4. get_point(k, refpt,r,a,nx,ny,cells,samples)
  • 2.5. button_callback()
  • 2.6. create_figure(stack_montage_flag)
  • 2.7. generate_stack_montage(chk_box_marker_sm, rb_imtech_val, LABELS_MARKERS)
  • 2.8. generate_image_tSNE(chk_box_marker,rb_val,rb_rs_val, rb_shf_val,rb_imtech_val,mc,wc,LABELS_MARKERS)
  • 2.9. draw_tSNE_scatter(tsne1,file_name_hover,cluster_ms_list)
• 3. Requirements
  • 3.1. Minimum Hardware specifications
  • 3.2. Software requirements
• 4. Code Installation
  • 4.1. Download Mistic
  • 4.2. Preload user data
  • 4.3. Run Mistic
• 5. Mistic experiments
  • 5.1. Datasets used to test Mistic
  • 5.2. Non-small cell lung cancer
  • 5.3. Lung adenocarcinoma metastasis to lymph node
  • 5.4. Primary lung squamous cell carcinoma
  • 5.5. Tissue Microarray cores for Endometrial cancer
  • 5.6. Human FFPE Tonsil data
  • 5.7. Human FFPE Breast adenocarcinoma
  • 5.8. Human FFPE Tonsil demo data from Akoya
  • 5.9. Human Colorectal carcinoma
• 6. Vignettes on t-CyCIF data
  • 6.1. t-CyCIF image on Lung adenocarcinoma metastasis to lymph node
  • 6.2. t-CyCIF image on Primary lung squamous cell carcinoma
• 7. Vignettes on Vectra data
  • 7.1. PerkinElmer Vectra based NSCLC FoVs

Indices and tables

• Index

• Module Index

• Search Page