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["Method type",null,"Method","Recovery of live cell subpopulations?","Image-based genetic screening capabilities","Transcriptomics based on visual phenotypes","Number of recovery bins","Imaging modality","Single cell resolution?","Custom Hardware?","Dye-based disposable reagents?","Demonstrated scale / experiment (mammalian cells)","Time / experiment","Hardware requirements","Dye-based imaging reagents","Genetic engineering required","Notes","PMID"]
["Multi-well",null,"High content imaging","No","Yes","No","NA","Confocal, widefield","Yes","No","Yes","1e6 - 1e7","Hours - days","Specialized ultra-high throughput microscope; robotics for reagent preparation","Fluorescent probes","Fluorescent protein markers","Imaging batch effects may confound true differences between wells",26638068]
["In situ nucleic acid methods",null,"MERFISH","No","Yes","Yes","NA","Confocal, widefield","Yes","Yes","Yes","~8,000","~20 hours","Confocal scanning microscope or widefield microscope with custom-built microfluidics chamber","Array-derived probe library; fluorescent readout probes","None","Reads out RNA-based barcodes; confocal required for measuring RNA expression; limited number of RNA species per experiment; complex sample preparation workflow; for pooled library screens, imaging must be done at 60X due to low barcode signal","25858977, 29083401, 31085639"]
[null,null,"seqFISH+","No","No","Yes","NA","Confocal","Yes","Yes","Yes","200-500","Not reported","Confocal scanning microscope with custom-built microfluidics chamber","Array-derived probe library; fluorescent readout probes","None","Similar to MERFISH but more genes (~10,000) can be quantified",30911168]
[null,null,"in situ sequencing (transcriptomics)","No","No","Yes","NA","Confocal","Yes","Yes","Yes","Not reported","16 days","Confocal scanning microscope","Next-generation sequencing kit-derived fluorescent probes","None",null,"23852452, 24578530, 25675209"]
[null,null,"in situ sequencing (pooled optical screens)","No","Yes","No","NA","Widefield","Yes","No","Yes","~3,000,000","5 days","Standard widefield microscope","Next-generation sequencing kit-derived fluorescent probes","None","Sequences short stretches of cDNA using a microscope; complex sample preparation protocol must be re-optimized for different cell types and sample types",31626775]
["Photoactivation-based",null,"CLaP","Yes","Yes","Yes",2,"Confocal","Yes","No","Yes","100-1,000","Not reported","Confocal microscope","Biotin-4-fluorescein; Cy5-streptavidin","None",null,27198043]
[null,null,"Niche-seq","Yes","No","Yes",2,"Two-photon","No","No","No","1,000 -10,000","Not reported","Two-photon microscope","None","PA-GFP stably expressed","Sort cells by spatial location in lymph nodes",29217582]
[null,null,"Optomagnetic cell capture","Yes","Yes","Yes",2,"Confocal","Yes","Yes","Yes","5-30","Not reported","Confocal microscope, custom chamber","Biotin-4-fluorescein; magnetic bead coated with streptavadin","None",null,30969169]
[null,null,"Optical painting","Yes","Yes","Yes",2,"Confocal","Yes","Yes","Yes","10-150","Not reported","Custom confocal microscope","Antibody-conjugated quantum dots made in-house","None",null,27118210]
[null,null,"Photostick","Yes","Yes","Yes",2,"Widefield","Yes","No","Yes","10-100","Not reported","Widefield microscope with digital micromirror device","Cy3- or Cy5-SBED","None",null,25705368]
[null,null,"Visual Cell Sorting","Yes","Yes","Yes",4,"Widefield","Yes","No","No","160,000","12-15 hours","Widefield microscope with digital micromirror device","None","H3-Dendra2 or NLS-Dendra2x3 stably expressed",null,"Current Work"]

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["Table EV1"]
["Comparison of microscope-based methods that dissect the relationship between genetic perturbations or gene expression programs and visual phenotype. "]