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Test effects of FOV number and/or cell count on profile strength #2

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bethac07 opened this issue Feb 16, 2022 · 5 comments
Open
1 of 2 tasks

Test effects of FOV number and/or cell count on profile strength #2

bethac07 opened this issue Feb 16, 2022 · 5 comments
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Experiments Tracking experimental questions, results, or analysis

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@bethac07
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bethac07 commented Feb 16, 2022 •
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We have a qualitative difference between conditions that have higher FOV counts (20X, typically) those with lower FOV counts (10X, typically, though not exclusively). This matches previous work

A couple of complicating factors here though -

  1. 4 fields of 10X vs 9 fields of 20X may have equal numbers of cells, even with lower numbers of fields. We've always speculated that more fields is better data because more cells, but maybe it isn't - maybe it's more chances to get a really good segmentation, or some other thing we haven't thought of. Our previous experiments were all tested at the same magnification, with cell count and FOV count essentially perfectly correlated, so we have no data addressing this directly.
  2. It may truly be that other magnifications really are worse than our standard 20X, but right now we can't tell because we know that FOV count MAY be a contributing factor.

To address these, I think we need to do 2 things -

  • Subsample all the existing batches to all the applicable FOV counts we can - we have batches with 1, 2, 3, 4, and 9 sites, so we should subsample 9 site batches to 4, 3, 2, and 1 sites, subsample for site batches to 3, 2, 1 sites, etc. Because we are currently pretty sure that we can use the same recipe run for all the batches being subsampled to 4 sites, another one for all the batches subsampled to 3, etc, this is actually only 4 config files to generate and run.
  • Once we've done the above, for each vendor look at a 2x2 matrix - percent matching / percent replicating vs FOV count/ cell count. I think this will help us be more definitive about both questions above.
@bethac07 bethac07 added the Experiments Tracking experimental questions, results, or analysis label Feb 16, 2022
@bethac07 bethac07 mentioned this issue Feb 16, 2022
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@NasimJ
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NasimJ commented Feb 23, 2022 •
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If we want the subsamples to have overlap and only from the field numbers 1,2,3,4 then we could do this with 4 config files, otherwise, we would need more, because the fields in the config file is the field number, not the number of fields.

For the subsample to not have overlap (or have partial overlap), we could subsample 4 fields from 9 fields by choosing fields 2, 4, 6, and 8. To subsample 3 fields from 9 fields, we could choose fields 3, 5, and 7, and so on.

I think for this purpose we would want our subsamples to have overlap (to have the same cell numbers and to be the exact subsample of the category above it), but I think this is something to consider.

We may also want to consider the site location discussion from slack; there will be differences in the cell numbers if site 1 located in a corner vs the center of a well.

@NasimJ
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NasimJ commented Feb 23, 2022 •
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I went ahead and created the profiles for FoVs, with fields 1,2,3,4 and 4 config files.
The FoV profiles are made with sqlite files (so we can aggregate the data differently).

In making the profiles, I did not repeat what was existed in the previous profiles (i.e: I didn’t include the batches with only 1 site to the re-aggregation for subsample 1 site profiles --> this means the 1 site subsample batches include all the batches EXCEPT the ones that originally imaged at only 1 site [Scope1_Nikon_10X], and similarly did not include batches with only 4 site for re-aggregation for 4 site subsample, etc.--> this means the 4 site subsample batches only includes the batches with originally 9 sites that are now being re-aggregated for 4 sites); in metadata file, the rows for 1 site images per well were removed (Nikon 10X).

Site and Filed are used in the names are interchangeable.

@NasimJ
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NasimJ commented Mar 4, 2022

Percent Replicating and Matching

Scope_vendor FoV_Batch Plate_Name Sites_SubSampled Percent_Replicating Percent_Matching
MolDev 1siteSubSample_Scope1_MolDev_10X Plate2_PCO_6ch_4site_10XPA 1 17.8 9.302
MolDev 1siteSubSample_Scope1_MolDev_10X Plate3_PCO_6ch_4site_10XPA_Crest 1 23.3 13.953
MolDev 1siteSubSample_Scope1_MolDev_10X_4siteZ Plate3_PCO_6ch_4site_10XPA_Crestz 1 20 4.651
MolDev 1siteSubSample_Scope1_MolDev_20X_4site Plate3_PCO_6ch_4site_20XPA_Crestz 1 34.4 18.605
MolDev 1siteSubSample_Scope1_MolDev_20X_9site Plate2_PCO_6ch_9site_20XPA 1 27.8 9.302
MolDev 1siteSubSample_Scope1_MolDev_20X_9site Plate3_PCO_6ch_9site_20XPA_Crest 1 14.4 6.977
MolDev 2siteSubSample_Scope1_MolDev_10X Plate2_PCO_6ch_4site_10XPA 2 13.3 6.977
MolDev 2siteSubSample_Scope1_MolDev_10X Plate3_PCO_6ch_4site_10XPA_Crest 2 26.7 9.302
MolDev 2siteSubSample_Scope1_MolDev_10X_4siteZ Plate3_PCO_6ch_4site_10XPA_Crestz 2 36.7 11.628
MolDev 2siteSubSample_Scope1_MolDev_20X_4site Plate3_PCO_6ch_4site_20XPA_Crestz 2 27.8 11.628
MolDev 2siteSubSample_Scope1_MolDev_20X_9site Plate2_PCO_6ch_9site_20XPA 2 23.3 6.977
MolDev 2siteSubSample_Scope1_MolDev_20X_9site Plate3_PCO_6ch_9site_20XPA_Crest 2 37.8 6.977
MolDev 3siteSubSample_Scope1_MolDev_10X Plate2_PCO_6ch_4site_10XPA 3 22.2 9.302
MolDev 3siteSubSample_Scope1_MolDev_10X Plate3_PCO_6ch_4site_10XPA_Crest 3 30 11.628
MolDev 3siteSubSample_Scope1_MolDev_10X_4siteZ Plate3_PCO_6ch_4site_10XPA_Crestz 3 38.9 11.628
MolDev 3siteSubSample_Scope1_MolDev_20X_4site Plate3_PCO_6ch_4site_20XPA_Crestz 3 31.1 11.628
MolDev 3siteSubSample_Scope1_MolDev_20X_9site Plate2_PCO_6ch_9site_20XPA 3 32.2 9.302
MolDev 3siteSubSample_Scope1_MolDev_20X_9site Plate3_PCO_6ch_9site_20XPA_Crest 3 17.8 9.302
MolDev 4siteSubSample_Scope1_MolDev_20X_9site Plate2_PCO_6ch_9site_20XPA 4 34.4 6.977
MolDev 4siteSubSample_Scope1_MolDev_20X_9site Plate3_PCO_6ch_9site_20XPA_Crest 4 23.3 16.279
Nikon 1siteSubSample_Scope1_Nikon_20X BR00117061a 1 41.1 18.605
Nikon 1siteSubSample_Scope1_Nikon_20X BR00117062a 1 41.1 16.279
Nikon 1siteSubSample_Scope1_Nikon_20X BR00117063b 1 33.3 9.302
Nikon 2siteSubSample_Scope1_Nikon_20X BR00117061a 2 41.1 13.953
Nikon 2siteSubSample_Scope1_Nikon_20X BR00117062a 2 37.8 16.279
Nikon 2siteSubSample_Scope1_Nikon_20X BR00117063b 2 28.9 9.302
Nikon 3siteSubSample_Scope1_Nikon_20X BR00117061a 3 48.9 13.953
Nikon 3siteSubSample_Scope1_Nikon_20X BR00117062a 3 41.1 13.953
Nikon 3siteSubSample_Scope1_Nikon_20X BR00117063b 3 30 9.302
Nikon 4siteSubSample_Scope1_Nikon_20X BR00117061a 4 46.7 13.953
Nikon 4siteSubSample_Scope1_Nikon_20X BR00117062a 4 22.2 9.302
Nikon 4siteSubSample_Scope1_Nikon_20X BR00117063b 4 35.6 11.628
PE 1siteSubSample_Scope1_PE_Bin1_Confocal_1Plane CP_Broad_Phenix_C_BIN1_1Plane_P1 1 41.1 16.279
PE 1siteSubSample_Scope1_PE_Bin1_Confocal_1Plane CP_Broad_Phenix_C_BIN1_1Plane_P2 1 38.9 18.605
PE 1siteSubSample_Scope1_PE_Bin1_Confocal_1Plane CP_Broad_Phenix_C_BIN1_1Plane_P3 1 36.7 11.628
PE 1siteSubSample_Scope1_PE_Bin1_Confocal_1Plane CP_Broad_Phenix_C_BIN1_1Plane_P4 1 33.3 18.605
PE 1siteSubSample_Scope1_PE_Bin1_Confocal_3Plane CP_Broad_Phenix_C_BIN1_P1 1 26.7 9.302
PE 1siteSubSample_Scope1_PE_Bin1_Confocal_3Plane CP_Broad_Phenix_C_BIN1_P2 1 16.7 6.977
PE 1siteSubSample_Scope1_PE_Bin1_Confocal_3Plane CP_Broad_Phenix_C_BIN1_P3 1 37.8 13.953
PE 1siteSubSample_Scope1_PE_Bin1_Confocal_3Plane CP_Broad_Phenix_C_BIN1_P4 1 37.8 11.628
PE 1siteSubSample_Scope1_PE_Bin1_Widefield_1Plane CP_Broad_Phenix_NC_BIN1_1Plane_P1 1 13.3 6.977
PE 1siteSubSample_Scope1_PE_Bin1_Widefield_1Plane CP_Broad_Phenix_NC_BIN1_1Plane_P2 1 25.6 16.279
PE 1siteSubSample_Scope1_PE_Bin1_Widefield_1Plane CP_Broad_Phenix_NC_BIN1_1Plane_P3 1 7.8 4.651
PE 1siteSubSample_Scope1_PE_Bin1_Widefield_1Plane CP_Broad_Phenix_NC_BIN1_1Plane_P4 1 12.2 4.651
PE 1siteSubSample_Scope1_PE_Bin1_Widefield_3Plane CP_Broad_Phenix_NC_BIN1_P1 1 11.1 6.977
PE 1siteSubSample_Scope1_PE_Bin1_Widefield_3Plane CP_Broad_Phenix_NC_BIN1_P2 1 11.1 6.977
PE 1siteSubSample_Scope1_PE_Bin1_Widefield_3Plane CP_Broad_Phenix_NC_BIN1_P3 1 6.7 2.326
PE 1siteSubSample_Scope1_PE_Bin1_Widefield_3Plane CP_Broad_Phenix_NC_BIN1_P4 1 11.1 6.977
PE 1siteSubSample_Scope1_PE_Bin2_Confocal_1Plane CPBroadPhenixC1PlaneP1 1 45.6 16.279
PE 1siteSubSample_Scope1_PE_Bin2_Confocal_1Plane CPBroadPhenixC1PlaneP2 1 45.6 18.605
PE 1siteSubSample_Scope1_PE_Bin2_Confocal_1Plane CPBroadPhenixC1PlaneP3 1 41.1 13.953
PE 1siteSubSample_Scope1_PE_Bin2_Confocal_1Plane CPBroadPhenixC1PlaneP4 1 40 23.256
PE 1siteSubSample_Scope1_PE_Bin2_Confocal_3Plane CPBroadPhenixCP1 1 48.9 16.279
PE 1siteSubSample_Scope1_PE_Bin2_Confocal_3Plane CPBroadPhenixCP2 1 4.4 2.326
PE 1siteSubSample_Scope1_PE_Bin2_Confocal_3Plane CPBroadPhenixCP3 1 10 2.326
PE 1siteSubSample_Scope1_PE_Bin2_Confocal_3Plane CPBroadPhenixCP4 1 13.3 2.326
PE 1siteSubSample_Scope1_PE_Bin2_Widefield_1Plane CPBroadPhenixNC1PlaneP1 1 44.4 13.953
PE 1siteSubSample_Scope1_PE_Bin2_Widefield_1Plane CPBroadPhenixNC1PlaneP2 1 45.6 16.279
PE 1siteSubSample_Scope1_PE_Bin2_Widefield_1Plane CPBroadPhenixNC1PlaneP3 1 18.9 11.628
PE 1siteSubSample_Scope1_PE_Bin2_Widefield_1Plane CPBroadPhenixNC1PlaneP4 1 45.6 16.279
PE 1siteSubSample_Scope1_PE_Bin2_Widefield_3Plane CPBroadPhenixNCP1 1 42.2 13.953
PE 1siteSubSample_Scope1_PE_Bin2_Widefield_3Plane CPBroadPhenixNCP2 1 45.6 18.605
PE 1siteSubSample_Scope1_PE_Bin2_Widefield_3Plane CPBroadPhenixNCP3 1 17.8 11.628
PE 1siteSubSample_Scope1_PE_Bin2_Widefield_3Plane CPBroadPhenixNCP4 1 43.3 16.279
PE 2siteSubSample_Scope1_PE_Bin1_Confocal_1Plane CP_Broad_Phenix_C_BIN1_1Plane_P1 2 40 16.279
PE 2siteSubSample_Scope1_PE_Bin1_Confocal_1Plane CP_Broad_Phenix_C_BIN1_1Plane_P2 2 28.9 16.279
PE 2siteSubSample_Scope1_PE_Bin1_Confocal_1Plane CP_Broad_Phenix_C_BIN1_1Plane_P3 2 42.2 13.953
PE 2siteSubSample_Scope1_PE_Bin1_Confocal_1Plane CP_Broad_Phenix_C_BIN1_1Plane_P4 2 24.4 13.953
PE 2siteSubSample_Scope1_PE_Bin1_Confocal_3Plane CP_Broad_Phenix_C_BIN1_P1 2 24.4 9.302
PE 2siteSubSample_Scope1_PE_Bin1_Confocal_3Plane CP_Broad_Phenix_C_BIN1_P2 2 46.7 20.93
PE 2siteSubSample_Scope1_PE_Bin1_Confocal_3Plane CP_Broad_Phenix_C_BIN1_P3 2 31.1 16.279
PE 2siteSubSample_Scope1_PE_Bin1_Confocal_3Plane CP_Broad_Phenix_C_BIN1_P4 2 31.1 16.279
PE 2siteSubSample_Scope1_PE_Bin1_Widefield_1Plane CP_Broad_Phenix_NC_BIN1_1Plane_P1 2 18.9 4.651
PE 2siteSubSample_Scope1_PE_Bin1_Widefield_1Plane CP_Broad_Phenix_NC_BIN1_1Plane_P2 2 11.1 9.302
PE 2siteSubSample_Scope1_PE_Bin1_Widefield_1Plane CP_Broad_Phenix_NC_BIN1_1Plane_P3 2 34.4 9.302
PE 2siteSubSample_Scope1_PE_Bin1_Widefield_1Plane CP_Broad_Phenix_NC_BIN1_1Plane_P4 2 18.9 11.628
PE 2siteSubSample_Scope1_PE_Bin1_Widefield_3Plane CP_Broad_Phenix_NC_BIN1_P1 2 34.4 13.953
PE 2siteSubSample_Scope1_PE_Bin1_Widefield_3Plane CP_Broad_Phenix_NC_BIN1_P2 2 28.9 11.628
PE 2siteSubSample_Scope1_PE_Bin1_Widefield_3Plane CP_Broad_Phenix_NC_BIN1_P3 2 24.4 16.279
PE 2siteSubSample_Scope1_PE_Bin1_Widefield_3Plane CP_Broad_Phenix_NC_BIN1_P4 2 18.9 6.977
PE 2siteSubSample_Scope1_PE_Bin2_Confocal_1Plane CPBroadPhenixC1PlaneP1 2 38.9 16.279
PE 2siteSubSample_Scope1_PE_Bin2_Confocal_1Plane CPBroadPhenixC1PlaneP2 2 34.4 9.302
PE 2siteSubSample_Scope1_PE_Bin2_Confocal_1Plane CPBroadPhenixC1PlaneP3 2 21.1 4.651
PE 2siteSubSample_Scope1_PE_Bin2_Confocal_1Plane CPBroadPhenixC1PlaneP4 2 37.8 11.628
PE 2siteSubSample_Scope1_PE_Bin2_Confocal_3Plane CPBroadPhenixCP1 2 42.2 18.605
PE 2siteSubSample_Scope1_PE_Bin2_Confocal_3Plane CPBroadPhenixCP2 2 12.2 9.302
PE 2siteSubSample_Scope1_PE_Bin2_Confocal_3Plane CPBroadPhenixCP3 2 48.9 20.93
PE 2siteSubSample_Scope1_PE_Bin2_Confocal_3Plane CPBroadPhenixCP4 2 46.7 18.605
PE 2siteSubSample_Scope1_PE_Bin2_Widefield_1Plane CPBroadPhenixNC1PlaneP1 2 36.7 11.628
PE 2siteSubSample_Scope1_PE_Bin2_Widefield_1Plane CPBroadPhenixNC1PlaneP2 2 51.1 16.279
PE 2siteSubSample_Scope1_PE_Bin2_Widefield_1Plane CPBroadPhenixNC1PlaneP3 2 44.4 13.953
PE 2siteSubSample_Scope1_PE_Bin2_Widefield_1Plane CPBroadPhenixNC1PlaneP4 2 43.3 18.605
PE 2siteSubSample_Scope1_PE_Bin2_Widefield_3Plane CPBroadPhenixNCP1 2 35.6 16.279
PE 2siteSubSample_Scope1_PE_Bin2_Widefield_3Plane CPBroadPhenixNCP2 2 27.8 11.628
PE 2siteSubSample_Scope1_PE_Bin2_Widefield_3Plane CPBroadPhenixNCP3 2 35.6 9.302
PE 2siteSubSample_Scope1_PE_Bin2_Widefield_3Plane CPBroadPhenixNCP4 2 37.8 16.279
Yokogawa_Japan 1siteSubSample_Scope1_Yokogawa_Japan_20X 20201021T092317 1 38.9 13.953
Yokogawa_Japan 1siteSubSample_Scope1_Yokogawa_Japan_40X 20201020T134356 1 25.6 16.279
Yokogawa_Japan 2siteSubSample_Scope1_Yokogawa_Japan_20X 20201021T092317 2 46.7 18.605
Yokogawa_Japan 3siteSubSample_Scope1_Yokogawa_Japan_20X 20201021T092317 3 47.8 18.605
Yokogawa_Japan 4siteSubSample_Scope1_Yokogawa_Japan_20X 20201021T092317 4 13.3 6.977
Yokogawa_US 1siteSubSample_Scope1_Yokogawa_US_10X BRO0117014_10x 1 38.9 13.953
Yokogawa_US 1siteSubSample_Scope1_Yokogawa_US_20X_5Ch BRO0117033_20xb 1 17.8 11.628
Yokogawa_US 1siteSubSample_Scope1_Yokogawa_US_20X_5Ch BRO0117056_20x 1 3.3 0
Yokogawa_US 1siteSubSample_Scope1_Yokogawa_US_20X_5Ch_12Z BRO0117056_20xb 1 37.8 11.628
Yokogawa_US 1siteSubSample_Scope1_Yokogawa_US_20X_6Ch_BRO0117059 BRO0117059_20X 1 44.9 19.048
Yokogawa_US 1siteSubSample_Scope1_Yokogawa_US_20X_6Ch_BRO01177034 BRO01177034_20x 1 45.6 13.953
Yokogawa_US 1siteSubSample_Scope1_Yokogawa_US_40X_BRO0117059 BRO0117059_40x 1 28.9 11.628
Yokogawa_US 2siteSubSample_Scope1_Yokogawa_US_10X BRO0117014_10x 2 38.9 18.605
Yokogawa_US 2siteSubSample_Scope1_Yokogawa_US_20X_5Ch BRO0117033_20xb 2 36.7 13.953
Yokogawa_US 2siteSubSample_Scope1_Yokogawa_US_20X_5Ch BRO0117056_20x 2 31.1 16.279
Yokogawa_US 2siteSubSample_Scope1_Yokogawa_US_20X_5Ch_12Z BRO0117056_20xb 2 34.4 11.628
Yokogawa_US 2siteSubSample_Scope1_Yokogawa_US_20X_6Ch_BRO0117059 BRO0117059_20X 2 46.7 16.279
Yokogawa_US 2siteSubSample_Scope1_Yokogawa_US_20X_6Ch_BRO01177034 BRO01177034_20x 2 45.6 18.605
Yokogawa_US 2siteSubSample_Scope1_Yokogawa_US_40X_BRO0117059 BRO0117059_40x 2 28.9 11.628
Yokogawa_US 3siteSubSample_Scope1_Yokogawa_US_10X BRO0117014_10x 3 42.2 18.605
Yokogawa_US 3siteSubSample_Scope1_Yokogawa_US_20X_5Ch BRO0117033_20xb 3 10 6.977
Yokogawa_US 3siteSubSample_Scope1_Yokogawa_US_20X_5Ch BRO0117056_20x 3 38.9 16.279
Yokogawa_US 3siteSubSample_Scope1_Yokogawa_US_20X_5Ch_12Z BRO0117056_20xb 3 51.1 20.93
Yokogawa_US 3siteSubSample_Scope1_Yokogawa_US_20X_6Ch_BRO0117059 BRO0117059_20X 3 34.4 13.953
Yokogawa_US 3siteSubSample_Scope1_Yokogawa_US_20X_6Ch_BRO01177034 BRO01177034_20x 3 46.7 16.279
Yokogawa_US 3siteSubSample_Scope1_Yokogawa_US_40X_BRO0117059 BRO0117059_40x 3 38.9 11.628
Yokogawa_US 4siteSubSample_Scope1_Yokogawa_US_20X_5Ch BRO0117033_20xb 4 37.8 16.279
Yokogawa_US 4siteSubSample_Scope1_Yokogawa_US_20X_5Ch BRO0117056_20x 4 38.9 18.605
Yokogawa_US 4siteSubSample_Scope1_Yokogawa_US_20X_5Ch_12Z BRO0117056_20xb 4 44.4 20.93
Yokogawa_US 4siteSubSample_Scope1_Yokogawa_US_20X_6Ch_BRO0117059 BRO0117059_20X 4 21.1 4.651
Yokogawa_US 4siteSubSample_Scope1_Yokogawa_US_20X_6Ch_BRO01177034 BRO01177034_20x 4 21.1 9.302
Yokogawa_US 4siteSubSample_Scope1_Yokogawa_US_40X_BRO0117059 BRO0117059_40x 4 35.6 13.953

Percent replicating

Scope_vendor FoV_Batch Plate_Name Sites_SubSampled Percent_Replicating
MolDev 1siteSubSample_Scope1_MolDev_10X Plate2_PCO_6ch_4site_10XPA 1 17.8
MolDev 1siteSubSample_Scope1_MolDev_10X Plate3_PCO_6ch_4site_10XPA_Crest 1 23.3
MolDev 1siteSubSample_Scope1_MolDev_10X_4siteZ Plate3_PCO_6ch_4site_10XPA_Crestz 1 20
MolDev 1siteSubSample_Scope1_MolDev_20X_4site Plate3_PCO_6ch_4site_20XPA_Crestz 1 34.4
MolDev 1siteSubSample_Scope1_MolDev_20X_9site Plate2_PCO_6ch_9site_20XPA 1 27.8
MolDev 1siteSubSample_Scope1_MolDev_20X_9site Plate3_PCO_6ch_9site_20XPA_Crest 1 14.4
MolDev 2siteSubSample_Scope1_MolDev_10X Plate2_PCO_6ch_4site_10XPA 2 13.3
MolDev 2siteSubSample_Scope1_MolDev_10X Plate3_PCO_6ch_4site_10XPA_Crest 2 26.7
MolDev 2siteSubSample_Scope1_MolDev_10X_4siteZ Plate3_PCO_6ch_4site_10XPA_Crestz 2 36.7
MolDev 2siteSubSample_Scope1_MolDev_20X_4site Plate3_PCO_6ch_4site_20XPA_Crestz 2 27.8
MolDev 2siteSubSample_Scope1_MolDev_20X_9site Plate2_PCO_6ch_9site_20XPA 2 23.3
MolDev 2siteSubSample_Scope1_MolDev_20X_9site Plate3_PCO_6ch_9site_20XPA_Crest 2 37.8
MolDev 3siteSubSample_Scope1_MolDev_10X Plate2_PCO_6ch_4site_10XPA 3 22.2
MolDev 3siteSubSample_Scope1_MolDev_10X Plate3_PCO_6ch_4site_10XPA_Crest 3 30
MolDev 3siteSubSample_Scope1_MolDev_10X_4siteZ Plate3_PCO_6ch_4site_10XPA_Crestz 3 38.9
MolDev 3siteSubSample_Scope1_MolDev_20X_4site Plate3_PCO_6ch_4site_20XPA_Crestz 3 31.1
MolDev 3siteSubSample_Scope1_MolDev_20X_9site Plate2_PCO_6ch_9site_20XPA 3 32.2
MolDev 3siteSubSample_Scope1_MolDev_20X_9site Plate3_PCO_6ch_9site_20XPA_Crest 3 17.8
MolDev 4siteSubSample_Scope1_MolDev_20X_9site Plate2_PCO_6ch_9site_20XPA 4 34.4
MolDev 4siteSubSample_Scope1_MolDev_20X_9site Plate3_PCO_6ch_9site_20XPA_Crest 4 23.3
Nikon 1siteSubSample_Scope1_Nikon_20X BR00117061a 1 41.1
Nikon 1siteSubSample_Scope1_Nikon_20X BR00117062a 1 41.1
Nikon 1siteSubSample_Scope1_Nikon_20X BR00117063b 1 33.3
Nikon 2siteSubSample_Scope1_Nikon_20X BR00117061a 2 41.1
Nikon 2siteSubSample_Scope1_Nikon_20X BR00117062a 2 37.8
Nikon 2siteSubSample_Scope1_Nikon_20X BR00117063b 2 28.9
Nikon 3siteSubSample_Scope1_Nikon_20X BR00117061a 3 48.9
Nikon 3siteSubSample_Scope1_Nikon_20X BR00117062a 3 41.1
Nikon 3siteSubSample_Scope1_Nikon_20X BR00117063b 3 30
Nikon 4siteSubSample_Scope1_Nikon_20X BR00117061a 4 46.7
Nikon 4siteSubSample_Scope1_Nikon_20X BR00117062a 4 22.2
Nikon 4siteSubSample_Scope1_Nikon_20X BR00117063b 4 35.6
PE 1siteSubSample_Scope1_PE_Bin1_Confocal_1Plane CP_Broad_Phenix_C_BIN1_1Plane_P1 1 41.1
PE 1siteSubSample_Scope1_PE_Bin1_Confocal_1Plane CP_Broad_Phenix_C_BIN1_1Plane_P2 1 38.9
PE 1siteSubSample_Scope1_PE_Bin1_Confocal_1Plane CP_Broad_Phenix_C_BIN1_1Plane_P3 1 36.7
PE 1siteSubSample_Scope1_PE_Bin1_Confocal_1Plane CP_Broad_Phenix_C_BIN1_1Plane_P4 1 33.3
PE 1siteSubSample_Scope1_PE_Bin1_Confocal_3Plane CP_Broad_Phenix_C_BIN1_P1 1 26.7
PE 1siteSubSample_Scope1_PE_Bin1_Confocal_3Plane CP_Broad_Phenix_C_BIN1_P2 1 16.7
PE 1siteSubSample_Scope1_PE_Bin1_Confocal_3Plane CP_Broad_Phenix_C_BIN1_P3 1 37.8
PE 1siteSubSample_Scope1_PE_Bin1_Confocal_3Plane CP_Broad_Phenix_C_BIN1_P4 1 37.8
PE 1siteSubSample_Scope1_PE_Bin1_Widefield_1Plane CP_Broad_Phenix_NC_BIN1_1Plane_P1 1 13.3
PE 1siteSubSample_Scope1_PE_Bin1_Widefield_1Plane CP_Broad_Phenix_NC_BIN1_1Plane_P2 1 25.6
PE 1siteSubSample_Scope1_PE_Bin1_Widefield_1Plane CP_Broad_Phenix_NC_BIN1_1Plane_P3 1 7.8
PE 1siteSubSample_Scope1_PE_Bin1_Widefield_1Plane CP_Broad_Phenix_NC_BIN1_1Plane_P4 1 12.2
PE 1siteSubSample_Scope1_PE_Bin1_Widefield_3Plane CP_Broad_Phenix_NC_BIN1_P1 1 11.1
PE 1siteSubSample_Scope1_PE_Bin1_Widefield_3Plane CP_Broad_Phenix_NC_BIN1_P2 1 11.1
PE 1siteSubSample_Scope1_PE_Bin1_Widefield_3Plane CP_Broad_Phenix_NC_BIN1_P3 1 6.7
PE 1siteSubSample_Scope1_PE_Bin1_Widefield_3Plane CP_Broad_Phenix_NC_BIN1_P4 1 11.1
PE 1siteSubSample_Scope1_PE_Bin2_Confocal_1Plane CPBroadPhenixC1PlaneP1 1 45.6
PE 1siteSubSample_Scope1_PE_Bin2_Confocal_1Plane CPBroadPhenixC1PlaneP2 1 45.6
PE 1siteSubSample_Scope1_PE_Bin2_Confocal_1Plane CPBroadPhenixC1PlaneP3 1 41.1
PE 1siteSubSample_Scope1_PE_Bin2_Confocal_1Plane CPBroadPhenixC1PlaneP4 1 40
PE 1siteSubSample_Scope1_PE_Bin2_Confocal_3Plane CPBroadPhenixCP1 1 48.9
PE 1siteSubSample_Scope1_PE_Bin2_Confocal_3Plane CPBroadPhenixCP2 1 4.4
PE 1siteSubSample_Scope1_PE_Bin2_Confocal_3Plane CPBroadPhenixCP3 1 10
PE 1siteSubSample_Scope1_PE_Bin2_Confocal_3Plane CPBroadPhenixCP4 1 13.3
PE 1siteSubSample_Scope1_PE_Bin2_Widefield_1Plane CPBroadPhenixNC1PlaneP1 1 44.4
PE 1siteSubSample_Scope1_PE_Bin2_Widefield_1Plane CPBroadPhenixNC1PlaneP2 1 45.6
PE 1siteSubSample_Scope1_PE_Bin2_Widefield_1Plane CPBroadPhenixNC1PlaneP3 1 18.9
PE 1siteSubSample_Scope1_PE_Bin2_Widefield_1Plane CPBroadPhenixNC1PlaneP4 1 45.6
PE 1siteSubSample_Scope1_PE_Bin2_Widefield_3Plane CPBroadPhenixNCP1 1 42.2
PE 1siteSubSample_Scope1_PE_Bin2_Widefield_3Plane CPBroadPhenixNCP2 1 45.6
PE 1siteSubSample_Scope1_PE_Bin2_Widefield_3Plane CPBroadPhenixNCP3 1 17.8
PE 1siteSubSample_Scope1_PE_Bin2_Widefield_3Plane CPBroadPhenixNCP4 1 43.3
PE 2siteSubSample_Scope1_PE_Bin1_Confocal_1Plane CP_Broad_Phenix_C_BIN1_1Plane_P1 2 40
PE 2siteSubSample_Scope1_PE_Bin1_Confocal_1Plane CP_Broad_Phenix_C_BIN1_1Plane_P2 2 28.9
PE 2siteSubSample_Scope1_PE_Bin1_Confocal_1Plane CP_Broad_Phenix_C_BIN1_1Plane_P3 2 42.2
PE 2siteSubSample_Scope1_PE_Bin1_Confocal_1Plane CP_Broad_Phenix_C_BIN1_1Plane_P4 2 24.4
PE 2siteSubSample_Scope1_PE_Bin1_Confocal_3Plane CP_Broad_Phenix_C_BIN1_P1 2 24.4
PE 2siteSubSample_Scope1_PE_Bin1_Confocal_3Plane CP_Broad_Phenix_C_BIN1_P2 2 46.7
PE 2siteSubSample_Scope1_PE_Bin1_Confocal_3Plane CP_Broad_Phenix_C_BIN1_P3 2 31.1
PE 2siteSubSample_Scope1_PE_Bin1_Confocal_3Plane CP_Broad_Phenix_C_BIN1_P4 2 31.1
PE 2siteSubSample_Scope1_PE_Bin1_Widefield_1Plane CP_Broad_Phenix_NC_BIN1_1Plane_P1 2 18.9
PE 2siteSubSample_Scope1_PE_Bin1_Widefield_1Plane CP_Broad_Phenix_NC_BIN1_1Plane_P2 2 11.1
PE 2siteSubSample_Scope1_PE_Bin1_Widefield_1Plane CP_Broad_Phenix_NC_BIN1_1Plane_P3 2 34.4
PE 2siteSubSample_Scope1_PE_Bin1_Widefield_1Plane CP_Broad_Phenix_NC_BIN1_1Plane_P4 2 18.9
PE 2siteSubSample_Scope1_PE_Bin1_Widefield_3Plane CP_Broad_Phenix_NC_BIN1_P1 2 34.4
PE 2siteSubSample_Scope1_PE_Bin1_Widefield_3Plane CP_Broad_Phenix_NC_BIN1_P2 2 28.9
PE 2siteSubSample_Scope1_PE_Bin1_Widefield_3Plane CP_Broad_Phenix_NC_BIN1_P3 2 24.4
PE 2siteSubSample_Scope1_PE_Bin1_Widefield_3Plane CP_Broad_Phenix_NC_BIN1_P4 2 18.9
PE 2siteSubSample_Scope1_PE_Bin2_Confocal_1Plane CPBroadPhenixC1PlaneP1 2 38.9
PE 2siteSubSample_Scope1_PE_Bin2_Confocal_1Plane CPBroadPhenixC1PlaneP2 2 34.4
PE 2siteSubSample_Scope1_PE_Bin2_Confocal_1Plane CPBroadPhenixC1PlaneP3 2 21.1
PE 2siteSubSample_Scope1_PE_Bin2_Confocal_1Plane CPBroadPhenixC1PlaneP4 2 37.8
PE 2siteSubSample_Scope1_PE_Bin2_Confocal_3Plane CPBroadPhenixCP1 2 42.2
PE 2siteSubSample_Scope1_PE_Bin2_Confocal_3Plane CPBroadPhenixCP2 2 12.2
PE 2siteSubSample_Scope1_PE_Bin2_Confocal_3Plane CPBroadPhenixCP3 2 48.9
PE 2siteSubSample_Scope1_PE_Bin2_Confocal_3Plane CPBroadPhenixCP4 2 46.7
PE 2siteSubSample_Scope1_PE_Bin2_Widefield_1Plane CPBroadPhenixNC1PlaneP1 2 36.7
PE 2siteSubSample_Scope1_PE_Bin2_Widefield_1Plane CPBroadPhenixNC1PlaneP2 2 51.1
PE 2siteSubSample_Scope1_PE_Bin2_Widefield_1Plane CPBroadPhenixNC1PlaneP3 2 44.4
PE 2siteSubSample_Scope1_PE_Bin2_Widefield_1Plane CPBroadPhenixNC1PlaneP4 2 43.3
PE 2siteSubSample_Scope1_PE_Bin2_Widefield_3Plane CPBroadPhenixNCP1 2 35.6
PE 2siteSubSample_Scope1_PE_Bin2_Widefield_3Plane CPBroadPhenixNCP2 2 27.8
PE 2siteSubSample_Scope1_PE_Bin2_Widefield_3Plane CPBroadPhenixNCP3 2 35.6
PE 2siteSubSample_Scope1_PE_Bin2_Widefield_3Plane CPBroadPhenixNCP4 2 37.8
Yokogawa_Japan 1siteSubSample_Scope1_Yokogawa_Japan_20X 20201021T092317 1 38.9
Yokogawa_Japan 1siteSubSample_Scope1_Yokogawa_Japan_40X 20201020T134356 1 25.6
Yokogawa_Japan 2siteSubSample_Scope1_Yokogawa_Japan_20X 20201021T092317 2 46.7
Yokogawa_Japan 3siteSubSample_Scope1_Yokogawa_Japan_20X 20201021T092317 3 47.8
Yokogawa_Japan 4siteSubSample_Scope1_Yokogawa_Japan_20X 20201021T092317 4 13.3
Yokogawa_US 1siteSubSample_Scope1_Yokogawa_US_10X BRO0117014_10x 1 38.9
Yokogawa_US 1siteSubSample_Scope1_Yokogawa_US_20X_5Ch BRO0117033_20xb 1 17.8
Yokogawa_US 1siteSubSample_Scope1_Yokogawa_US_20X_5Ch BRO0117056_20x 1 3.3
Yokogawa_US 1siteSubSample_Scope1_Yokogawa_US_20X_5Ch_12Z BRO0117056_20xb 1 37.8
Yokogawa_US 1siteSubSample_Scope1_Yokogawa_US_20X_6Ch_BRO0117059 BRO0117059_20X 1 44.9
Yokogawa_US 1siteSubSample_Scope1_Yokogawa_US_20X_6Ch_BRO01177034 BRO01177034_20x 1 45.6
Yokogawa_US 1siteSubSample_Scope1_Yokogawa_US_40X_BRO0117059 BRO0117059_40x 1 28.9
Yokogawa_US 2siteSubSample_Scope1_Yokogawa_US_10X BRO0117014_10x 2 38.9
Yokogawa_US 2siteSubSample_Scope1_Yokogawa_US_20X_5Ch BRO0117033_20xb 2 36.7
Yokogawa_US 2siteSubSample_Scope1_Yokogawa_US_20X_5Ch BRO0117056_20x 2 31.1
Yokogawa_US 2siteSubSample_Scope1_Yokogawa_US_20X_5Ch_12Z BRO0117056_20xb 2 34.4
Yokogawa_US 2siteSubSample_Scope1_Yokogawa_US_20X_6Ch_BRO0117059 BRO0117059_20X 2 46.7
Yokogawa_US 2siteSubSample_Scope1_Yokogawa_US_20X_6Ch_BRO01177034 BRO01177034_20x 2 45.6
Yokogawa_US 2siteSubSample_Scope1_Yokogawa_US_40X_BRO0117059 BRO0117059_40x 2 28.9
Yokogawa_US 3siteSubSample_Scope1_Yokogawa_US_10X BRO0117014_10x 3 42.2
Yokogawa_US 3siteSubSample_Scope1_Yokogawa_US_20X_5Ch BRO0117033_20xb 3 10
Yokogawa_US 3siteSubSample_Scope1_Yokogawa_US_20X_5Ch BRO0117056_20x 3 38.9
Yokogawa_US 3siteSubSample_Scope1_Yokogawa_US_20X_5Ch_12Z BRO0117056_20xb 3 51.1
Yokogawa_US 3siteSubSample_Scope1_Yokogawa_US_20X_6Ch_BRO0117059 BRO0117059_20X 3 34.4
Yokogawa_US 3siteSubSample_Scope1_Yokogawa_US_20X_6Ch_BRO01177034 BRO01177034_20x 3 46.7
Yokogawa_US 3siteSubSample_Scope1_Yokogawa_US_40X_BRO0117059 BRO0117059_40x 3 38.9
Yokogawa_US 4siteSubSample_Scope1_Yokogawa_US_20X_5Ch BRO0117033_20xb 4 37.8
Yokogawa_US 4siteSubSample_Scope1_Yokogawa_US_20X_5Ch BRO0117056_20x 4 38.9
Yokogawa_US 4siteSubSample_Scope1_Yokogawa_US_20X_5Ch_12Z BRO0117056_20xb 4 44.4
Yokogawa_US 4siteSubSample_Scope1_Yokogawa_US_20X_6Ch_BRO0117059 BRO0117059_20X 4 21.1
Yokogawa_US 4siteSubSample_Scope1_Yokogawa_US_20X_6Ch_BRO01177034 BRO01177034_20x 4 21.1
Yokogawa_US 4siteSubSample_Scope1_Yokogawa_US_40X_BRO0117059 BRO0117059_40x 4 35.6
Distribution plots

1 FoV_percent_replicating

Percent Matching:

Scope_vendor FoV_Batch Plate_Name Sites_SubSampled Percent_Matching
MolDev 1siteSubSample_Scope1_MolDev_10X Plate2_PCO_6ch_4site_10XPA 1 9.302
MolDev 1siteSubSample_Scope1_MolDev_10X Plate3_PCO_6ch_4site_10XPA_Crest 1 13.953
MolDev 1siteSubSample_Scope1_MolDev_10X_4siteZ Plate3_PCO_6ch_4site_10XPA_Crestz 1 4.651
MolDev 1siteSubSample_Scope1_MolDev_20X_4site Plate3_PCO_6ch_4site_20XPA_Crestz 1 18.605
MolDev 1siteSubSample_Scope1_MolDev_20X_9site Plate2_PCO_6ch_9site_20XPA 1 9.302
MolDev 1siteSubSample_Scope1_MolDev_20X_9site Plate3_PCO_6ch_9site_20XPA_Crest 1 6.977
MolDev 2siteSubSample_Scope1_MolDev_10X Plate2_PCO_6ch_4site_10XPA 2 6.977
MolDev 2siteSubSample_Scope1_MolDev_10X Plate3_PCO_6ch_4site_10XPA_Crest 2 9.302
MolDev 2siteSubSample_Scope1_MolDev_10X_4siteZ Plate3_PCO_6ch_4site_10XPA_Crestz 2 11.628
MolDev 2siteSubSample_Scope1_MolDev_20X_4site Plate3_PCO_6ch_4site_20XPA_Crestz 2 11.628
MolDev 2siteSubSample_Scope1_MolDev_20X_9site Plate2_PCO_6ch_9site_20XPA 2 6.977
MolDev 2siteSubSample_Scope1_MolDev_20X_9site Plate3_PCO_6ch_9site_20XPA_Crest 2 6.977
MolDev 3siteSubSample_Scope1_MolDev_10X Plate2_PCO_6ch_4site_10XPA 3 9.302
MolDev 3siteSubSample_Scope1_MolDev_10X Plate3_PCO_6ch_4site_10XPA_Crest 3 11.628
MolDev 3siteSubSample_Scope1_MolDev_10X_4siteZ Plate3_PCO_6ch_4site_10XPA_Crestz 3 11.628
MolDev 3siteSubSample_Scope1_MolDev_20X_4site Plate3_PCO_6ch_4site_20XPA_Crestz 3 11.628
MolDev 3siteSubSample_Scope1_MolDev_20X_9site Plate2_PCO_6ch_9site_20XPA 3 9.302
MolDev 3siteSubSample_Scope1_MolDev_20X_9site Plate3_PCO_6ch_9site_20XPA_Crest 3 9.302
MolDev 4siteSubSample_Scope1_MolDev_20X_9site Plate2_PCO_6ch_9site_20XPA 4 6.977
MolDev 4siteSubSample_Scope1_MolDev_20X_9site Plate3_PCO_6ch_9site_20XPA_Crest 4 16.279
Nikon 1siteSubSample_Scope1_Nikon_20X BR00117061a 1 18.605
Nikon 1siteSubSample_Scope1_Nikon_20X BR00117062a 1 16.279
Nikon 1siteSubSample_Scope1_Nikon_20X BR00117063b 1 9.302
Nikon 2siteSubSample_Scope1_Nikon_20X BR00117061a 2 13.953
Nikon 2siteSubSample_Scope1_Nikon_20X BR00117062a 2 16.279
Nikon 2siteSubSample_Scope1_Nikon_20X BR00117063b 2 9.302
Nikon 3siteSubSample_Scope1_Nikon_20X BR00117061a 3 13.953
Nikon 3siteSubSample_Scope1_Nikon_20X BR00117062a 3 13.953
Nikon 3siteSubSample_Scope1_Nikon_20X BR00117063b 3 9.302
Nikon 4siteSubSample_Scope1_Nikon_20X BR00117061a 4 13.953
Nikon 4siteSubSample_Scope1_Nikon_20X BR00117062a 4 9.302
Nikon 4siteSubSample_Scope1_Nikon_20X BR00117063b 4 11.628
PE 1siteSubSample_Scope1_PE_Bin1_Confocal_1Plane CP_Broad_Phenix_C_BIN1_1Plane_P1 1 16.279
PE 1siteSubSample_Scope1_PE_Bin1_Confocal_1Plane CP_Broad_Phenix_C_BIN1_1Plane_P2 1 18.605
PE 1siteSubSample_Scope1_PE_Bin1_Confocal_1Plane CP_Broad_Phenix_C_BIN1_1Plane_P3 1 11.628
PE 1siteSubSample_Scope1_PE_Bin1_Confocal_1Plane CP_Broad_Phenix_C_BIN1_1Plane_P4 1 18.605
PE 1siteSubSample_Scope1_PE_Bin1_Confocal_3Plane CP_Broad_Phenix_C_BIN1_P1 1 9.302
PE 1siteSubSample_Scope1_PE_Bin1_Confocal_3Plane CP_Broad_Phenix_C_BIN1_P2 1 6.977
PE 1siteSubSample_Scope1_PE_Bin1_Confocal_3Plane CP_Broad_Phenix_C_BIN1_P3 1 13.953
PE 1siteSubSample_Scope1_PE_Bin1_Confocal_3Plane CP_Broad_Phenix_C_BIN1_P4 1 11.628
PE 1siteSubSample_Scope1_PE_Bin1_Widefield_1Plane CP_Broad_Phenix_NC_BIN1_1Plane_P1 1 6.977
PE 1siteSubSample_Scope1_PE_Bin1_Widefield_1Plane CP_Broad_Phenix_NC_BIN1_1Plane_P2 1 16.279
PE 1siteSubSample_Scope1_PE_Bin1_Widefield_1Plane CP_Broad_Phenix_NC_BIN1_1Plane_P3 1 4.651
PE 1siteSubSample_Scope1_PE_Bin1_Widefield_1Plane CP_Broad_Phenix_NC_BIN1_1Plane_P4 1 4.651
PE 1siteSubSample_Scope1_PE_Bin1_Widefield_3Plane CP_Broad_Phenix_NC_BIN1_P1 1 6.977
PE 1siteSubSample_Scope1_PE_Bin1_Widefield_3Plane CP_Broad_Phenix_NC_BIN1_P2 1 6.977
PE 1siteSubSample_Scope1_PE_Bin1_Widefield_3Plane CP_Broad_Phenix_NC_BIN1_P3 1 2.326
PE 1siteSubSample_Scope1_PE_Bin1_Widefield_3Plane CP_Broad_Phenix_NC_BIN1_P4 1 6.977
PE 1siteSubSample_Scope1_PE_Bin2_Confocal_1Plane CPBroadPhenixC1PlaneP1 1 16.279
PE 1siteSubSample_Scope1_PE_Bin2_Confocal_1Plane CPBroadPhenixC1PlaneP2 1 18.605
PE 1siteSubSample_Scope1_PE_Bin2_Confocal_1Plane CPBroadPhenixC1PlaneP3 1 13.953
PE 1siteSubSample_Scope1_PE_Bin2_Confocal_1Plane CPBroadPhenixC1PlaneP4 1 23.256
PE 1siteSubSample_Scope1_PE_Bin2_Confocal_3Plane CPBroadPhenixCP1 1 16.279
PE 1siteSubSample_Scope1_PE_Bin2_Confocal_3Plane CPBroadPhenixCP2 1 2.326
PE 1siteSubSample_Scope1_PE_Bin2_Confocal_3Plane CPBroadPhenixCP3 1 2.326
PE 1siteSubSample_Scope1_PE_Bin2_Confocal_3Plane CPBroadPhenixCP4 1 2.326
PE 1siteSubSample_Scope1_PE_Bin2_Widefield_1Plane CPBroadPhenixNC1PlaneP1 1 13.953
PE 1siteSubSample_Scope1_PE_Bin2_Widefield_1Plane CPBroadPhenixNC1PlaneP2 1 16.279
PE 1siteSubSample_Scope1_PE_Bin2_Widefield_1Plane CPBroadPhenixNC1PlaneP3 1 11.628
PE 1siteSubSample_Scope1_PE_Bin2_Widefield_1Plane CPBroadPhenixNC1PlaneP4 1 16.279
PE 1siteSubSample_Scope1_PE_Bin2_Widefield_3Plane CPBroadPhenixNCP1 1 13.953
PE 1siteSubSample_Scope1_PE_Bin2_Widefield_3Plane CPBroadPhenixNCP2 1 18.605
PE 1siteSubSample_Scope1_PE_Bin2_Widefield_3Plane CPBroadPhenixNCP3 1 11.628
PE 1siteSubSample_Scope1_PE_Bin2_Widefield_3Plane CPBroadPhenixNCP4 1 16.279
PE 2siteSubSample_Scope1_PE_Bin1_Confocal_1Plane CP_Broad_Phenix_C_BIN1_1Plane_P1 2 16.279
PE 2siteSubSample_Scope1_PE_Bin1_Confocal_1Plane CP_Broad_Phenix_C_BIN1_1Plane_P2 2 16.279
PE 2siteSubSample_Scope1_PE_Bin1_Confocal_1Plane CP_Broad_Phenix_C_BIN1_1Plane_P3 2 13.953
PE 2siteSubSample_Scope1_PE_Bin1_Confocal_1Plane CP_Broad_Phenix_C_BIN1_1Plane_P4 2 13.953
PE 2siteSubSample_Scope1_PE_Bin1_Confocal_3Plane CP_Broad_Phenix_C_BIN1_P1 2 9.302
PE 2siteSubSample_Scope1_PE_Bin1_Confocal_3Plane CP_Broad_Phenix_C_BIN1_P2 2 20.93
PE 2siteSubSample_Scope1_PE_Bin1_Confocal_3Plane CP_Broad_Phenix_C_BIN1_P3 2 16.279
PE 2siteSubSample_Scope1_PE_Bin1_Confocal_3Plane CP_Broad_Phenix_C_BIN1_P4 2 16.279
PE 2siteSubSample_Scope1_PE_Bin1_Widefield_1Plane CP_Broad_Phenix_NC_BIN1_1Plane_P1 2 4.651
PE 2siteSubSample_Scope1_PE_Bin1_Widefield_1Plane CP_Broad_Phenix_NC_BIN1_1Plane_P2 2 9.302
PE 2siteSubSample_Scope1_PE_Bin1_Widefield_1Plane CP_Broad_Phenix_NC_BIN1_1Plane_P3 2 9.302
PE 2siteSubSample_Scope1_PE_Bin1_Widefield_1Plane CP_Broad_Phenix_NC_BIN1_1Plane_P4 2 11.628
PE 2siteSubSample_Scope1_PE_Bin1_Widefield_3Plane CP_Broad_Phenix_NC_BIN1_P1 2 13.953
PE 2siteSubSample_Scope1_PE_Bin1_Widefield_3Plane CP_Broad_Phenix_NC_BIN1_P2 2 11.628
PE 2siteSubSample_Scope1_PE_Bin1_Widefield_3Plane CP_Broad_Phenix_NC_BIN1_P3 2 16.279
PE 2siteSubSample_Scope1_PE_Bin1_Widefield_3Plane CP_Broad_Phenix_NC_BIN1_P4 2 6.977
PE 2siteSubSample_Scope1_PE_Bin2_Confocal_1Plane CPBroadPhenixC1PlaneP1 2 16.279
PE 2siteSubSample_Scope1_PE_Bin2_Confocal_1Plane CPBroadPhenixC1PlaneP2 2 9.302
PE 2siteSubSample_Scope1_PE_Bin2_Confocal_1Plane CPBroadPhenixC1PlaneP3 2 4.651
PE 2siteSubSample_Scope1_PE_Bin2_Confocal_1Plane CPBroadPhenixC1PlaneP4 2 11.628
PE 2siteSubSample_Scope1_PE_Bin2_Confocal_3Plane CPBroadPhenixCP1 2 18.605
PE 2siteSubSample_Scope1_PE_Bin2_Confocal_3Plane CPBroadPhenixCP2 2 9.302
PE 2siteSubSample_Scope1_PE_Bin2_Confocal_3Plane CPBroadPhenixCP3 2 20.93
PE 2siteSubSample_Scope1_PE_Bin2_Confocal_3Plane CPBroadPhenixCP4 2 18.605
PE 2siteSubSample_Scope1_PE_Bin2_Widefield_1Plane CPBroadPhenixNC1PlaneP1 2 11.628
PE 2siteSubSample_Scope1_PE_Bin2_Widefield_1Plane CPBroadPhenixNC1PlaneP2 2 16.279
PE 2siteSubSample_Scope1_PE_Bin2_Widefield_1Plane CPBroadPhenixNC1PlaneP3 2 13.953
PE 2siteSubSample_Scope1_PE_Bin2_Widefield_1Plane CPBroadPhenixNC1PlaneP4 2 18.605
PE 2siteSubSample_Scope1_PE_Bin2_Widefield_3Plane CPBroadPhenixNCP1 2 16.279
PE 2siteSubSample_Scope1_PE_Bin2_Widefield_3Plane CPBroadPhenixNCP2 2 11.628
PE 2siteSubSample_Scope1_PE_Bin2_Widefield_3Plane CPBroadPhenixNCP3 2 9.302
PE 2siteSubSample_Scope1_PE_Bin2_Widefield_3Plane CPBroadPhenixNCP4 2 16.279
Yokogawa_Japan 1siteSubSample_Scope1_Yokogawa_Japan_20X 20201021T092317 1 13.953
Yokogawa_Japan 1siteSubSample_Scope1_Yokogawa_Japan_40X 20201020T134356 1 16.279
Yokogawa_Japan 2siteSubSample_Scope1_Yokogawa_Japan_20X 20201021T092317 2 18.605
Yokogawa_Japan 3siteSubSample_Scope1_Yokogawa_Japan_20X 20201021T092317 3 18.605
Yokogawa_Japan 4siteSubSample_Scope1_Yokogawa_Japan_20X 20201021T092317 4 6.977
Yokogawa_US 1siteSubSample_Scope1_Yokogawa_US_10X BRO0117014_10x 1 13.953
Yokogawa_US 1siteSubSample_Scope1_Yokogawa_US_20X_5Ch BRO0117033_20xb 1 11.628
Yokogawa_US 1siteSubSample_Scope1_Yokogawa_US_20X_5Ch BRO0117056_20x 1 0
Yokogawa_US 1siteSubSample_Scope1_Yokogawa_US_20X_5Ch_12Z BRO0117056_20xb 1 11.628
Yokogawa_US 1siteSubSample_Scope1_Yokogawa_US_20X_6Ch_BRO0117059 BRO0117059_20X 1 19.048
Yokogawa_US 1siteSubSample_Scope1_Yokogawa_US_20X_6Ch_BRO01177034 BRO01177034_20x 1 13.953
Yokogawa_US 1siteSubSample_Scope1_Yokogawa_US_40X_BRO0117059 BRO0117059_40x 1 11.628
Yokogawa_US 2siteSubSample_Scope1_Yokogawa_US_10X BRO0117014_10x 2 18.605
Yokogawa_US 2siteSubSample_Scope1_Yokogawa_US_20X_5Ch BRO0117033_20xb 2 13.953
Yokogawa_US 2siteSubSample_Scope1_Yokogawa_US_20X_5Ch BRO0117056_20x 2 16.279
Yokogawa_US 2siteSubSample_Scope1_Yokogawa_US_20X_5Ch_12Z BRO0117056_20xb 2 11.628
Yokogawa_US 2siteSubSample_Scope1_Yokogawa_US_20X_6Ch_BRO0117059 BRO0117059_20X 2 16.279
Yokogawa_US 2siteSubSample_Scope1_Yokogawa_US_20X_6Ch_BRO01177034 BRO01177034_20x 2 18.605
Yokogawa_US 2siteSubSample_Scope1_Yokogawa_US_40X_BRO0117059 BRO0117059_40x 2 11.628
Yokogawa_US 3siteSubSample_Scope1_Yokogawa_US_10X BRO0117014_10x 3 18.605
Yokogawa_US 3siteSubSample_Scope1_Yokogawa_US_20X_5Ch BRO0117033_20xb 3 6.977
Yokogawa_US 3siteSubSample_Scope1_Yokogawa_US_20X_5Ch BRO0117056_20x 3 16.279
Yokogawa_US 3siteSubSample_Scope1_Yokogawa_US_20X_5Ch_12Z BRO0117056_20xb 3 20.93
Yokogawa_US 3siteSubSample_Scope1_Yokogawa_US_20X_6Ch_BRO0117059 BRO0117059_20X 3 13.953
Yokogawa_US 3siteSubSample_Scope1_Yokogawa_US_20X_6Ch_BRO01177034 BRO01177034_20x 3 16.279
Yokogawa_US 3siteSubSample_Scope1_Yokogawa_US_40X_BRO0117059 BRO0117059_40x 3 11.628
Yokogawa_US 4siteSubSample_Scope1_Yokogawa_US_20X_5Ch BRO0117033_20xb 4 16.279
Yokogawa_US 4siteSubSample_Scope1_Yokogawa_US_20X_5Ch BRO0117056_20x 4 18.605
Yokogawa_US 4siteSubSample_Scope1_Yokogawa_US_20X_5Ch_12Z BRO0117056_20xb 4 20.93
Yokogawa_US 4siteSubSample_Scope1_Yokogawa_US_20X_6Ch_BRO0117059 BRO0117059_20X 4 4.651
Yokogawa_US 4siteSubSample_Scope1_Yokogawa_US_20X_6Ch_BRO01177034 BRO01177034_20x 4 9.302
Yokogawa_US 4siteSubSample_Scope1_Yokogawa_US_40X_BRO0117059 BRO0117059_40x 4 13.953
Distribution plots

1 FoV_percent_matching

@NasimJ NasimJ mentioned this issue Mar 4, 2022
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@bethac07
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TODO - see if sphering (or whatever we end up replacing sphering with) helps to bring these numbers up

@bethac07
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Code that adds sphering https://github.com/carpenterlab/2022_Cimini_NatureProtocols/blob/main/notebooks/utils.py#L398-L419

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