| A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z | AA | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | Directory Structure Schema: | https://docs.google.com/spreadsheets/d/1fDxpEvln9o7P0YrTZPBxpTY98UkDuWEhmaMUFA8LNHE/edit#gid=1843407110 | |||||||||||||||||||||||||
2 | |||||||||||||||||||||||||||
3 | Options: required, optional, EPIC, n/a | ||||||||||||||||||||||||||
4 | Stereo-Seq | Visium (no probes) | Visium (with probes) | GeoMx (NGS) | GeoMx (nCounter) | HiFi | hrsTP-seq (DBiTSeq) | Xenium | Resolve | CosMx | MERFISH | Path | File name | File format | Data format | Data Schema | is from an instrument? | Manufacturer | Model | Derived by | Process version number | Instrument or program source | is QA? | Example | File or directory description | ||
5 | required | required | required | required | required | required | required | required | required | required | required | TOP/ | Top level directory | ||||||||||||||
6 | required RNAseq | required RNAseq (with probes) | required RNAseq (with probes) | n/a | n/a | n/a | n/a | n/a | n/a | n/a | Sequencing Files To Be Included | ||||||||||||||||
7 | required | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | Histology Files To Be Included | ||||||||||||||||
8 | required | see histology | required | required | required | required | required | required | required | required | required | TOP/extras/ | Folder for general lab-specific files related to the dataset | ||||||||||||||
9 | required | required | required | required | required | required | required | required | required | required | TOP/extras/ | microscope_hardware.json | https://www.protocols.io/view/getting-started-with-micro-meta-app-tutorial-36wgq7ddxvk5/v7/materials | 4DN-BINA-OME | no | micro-meta app | yes | A file generated by the micro-meta app that contains a description of the hardware components of the microscope. Email HuBMAP Consortium Help Desk <help@hubmapconsortium.org> if help is required in generating this document. | |||||||||
10 | optional | optional | optional | optional | optional | optional | optional | optional | optional | TOP/extras/ | microscope_settings.json | https://www.protocols.io/view/getting-started-with-micro-meta-app-tutorial-36wgq7ddxvk5/v7/materials | 4DN-BINA-OME | no | micro-meta app | yes | A file generated by the micro-meta app that contains a description of the settings that were used to acquire the image data. Email HuBMAP Consortium Help Desk <help@hubmapconsortium.org> if help is required in generating this document. | ||||||||||
11 | required | required | required | required | required | required | required | required | required | required | TOP/raw/ | All raw data files for the experiment. | |||||||||||||||
12 | required | required | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/raw/ | <slide ID>.gpr | GPR | no | 10X Genomics | GPR downloader | no | This is a 10X Genomics layout file that's generated by 10X and individualized for each Visium slide. This is a text file and can be generated using this 10X web form along with the unique 10X Visium slide ID. | |||||||||
13 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | n/a | TOP/raw/ | *_expMat_file.csv | |||||||||||||||
14 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | n/a | TOP/raw/ | *_fov_positions_file.csv | |||||||||||||||
15 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | n/a | TOP/raw/ | *_metadata_file.csv | |||||||||||||||
16 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | n/a | TOP/raw/ | *_tx_file.csv | |||||||||||||||
17 | n/a | n/a | required | required | n/a | n/a | n/a | n/a | n/a | n/a | TOP/raw/ | *_LabWorksheet.txt | txt | yes | NanoString | An Excel spreadsheet to refer to in setting up the library. This file documents all of the samples from a single collection plate. Generated by DSP run, prior to sequencing. | |||||||||||
18 | n/a | n/a | required | n/a | n/a | n/a | n/a | n/a | required | n/a | TOP/raw/ | *_config.ini | txt | For CosMx this would include: AtoMx server version module version acquisition instrument firmware version | yes | NanoString | Needed to generate the DCC file from the fastq file. Contains pipeline processing parameters. Generated by DSP run, prior to sequencing. | ||||||||||
19 | n/a | n/a | required | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/raw/ | *_SeqCodeIndices.csv | csv | A file with sample information needed by the Illumina software. Use the contents of the SeqCodeIndices.csv file to create a SampleSheet.csv for input to the Illumina sequencer. (NextSeq 1000/2000 users download a SampleSheet.csv and whitelist.txt instead of SeqCodeIndices.csv.) Generated by DSP run. | |||||||||||||
20 | n/a | n/a | optional | optional | n/a | optional | optional | required | n/a | TOP/raw/ | markers.csv | csv | name of fluorophor, vendor, channel | A csv file describing any morphology markers used to guide ROI and/or AOI selection. | |||||||||||||
21 | n/a | n/a | required | required | n/a | n/a | n/a | n/a | n/a | TOP/raw/ | *targets.pkc | pkc | The file listing probe barcode sequence and corresponding gene symbol or proteins targeted by that probe. This should be consistent for the same probe panel. | ||||||||||||||
22 | n/a | see RNAseq (with probes) | see RNAseq (with probes) | optional | n/a | optional | optional | optional | optional | TOP/raw/ | additional_panels_used.csv | csv | manufacturer, model/name, product code | If multiple commercial probe panels were used, then the primary probe panel should be selected in the "oligo_probe_panel" metadata field. The additional panels must be included in this file. Each panel record should include: manufacturer, model/name, product code. | |||||||||||||
23 | n/a | n/a | n/a | n/a | required | required | required | TOP/raw/ | gene_panel.csv | gene_id (ensembl ID), gene_name | The list of target genes. | ||||||||||||||||
24 | n/a | n/a | n/a | n/a | optional | optional | optional | optional | TOP/raw/ | custom_probe_set.csv | csv | gene_name, probe_seq, probe_id | This file should contain any custom probes used and must be included if the metadata field "is_custom_probes_used" is "Yes". The file should minimally include: target gene id, probe seq, probe id. The contents of this file are modeled after the 10x Genomics probe set file (see https://support.10xgenomics.com/spatial-gene-expression-ffpe/probe-sets/probe-set-file-descriptions/probe-set-file-descriptions#probe_set_csv_file). | ||||||||||||||
25 | n/a | n/a | n/a | n/a | optional | n/a | n/a | n/a | TOP/raw/ | custom_probe_set.bed | This is a BED file version of the custom probe set file. | ||||||||||||||||
26 | n/a | n/a | n/a | n/a | n/a | required | required | required | n/a | TOP/raw/ | transcript_locations.csv | csv | gene name, x, y, z (optional), quality score (optional) | The origin of the coordinate is 0,0 at the top left corner of the image. The file should include: gene name, x, y, z (optional), quality score (optional). It is expected that the first row in the file contains the column header. | |||||||||||||
27 | n/a | n/a | n/a | n/a | n/a | optional | required | optional | n/a | TOP/raw/ | custom_gene_list.csv | csv | gene name, ensemble ID | ||||||||||||||
28 | n/a | n/a | n/a | n/a | n/a | optional | optional | optional | n/a | TOP/raw/ | probes.csv | csv | Gene Ensembl_ID Coverage Codewords Annotation | A CSV file describing the probe panel used. This is tyipcally what's used to specific the probe set when ordering a probe panel for a Xenium run. | |||||||||||||
29 | n/a | n/a | n/a | n/a | n/a | required | n/a | n/a | n/a | TOP/raw/ | gene_panel.json | json | This is the JSON file describing the probes, as output from the xenium-ranger pipeline. | ||||||||||||||
30 | n/a | n/a | n/a | required | n/a | n/a | n/a | n/a | n/a | n/a | TOP/raw/ | *.rcc | The reporter code count from the nCounter. This is the readout, akin to the fastq files from the NGS workflow. There will be one RCC file per AOI. | ||||||||||||||
31 | n/a | n/a | n/a | required | n/a | n/a | n/a | n/a | n/a | TOP/raw/ | *.cdf | Cartridge definition file for the nCounter. | |||||||||||||||
32 | optional | TOP/raw/ | micron_to_mosaic_pixel_transform.csv | Matrix used to transform from pixels to physical distance. | |||||||||||||||||||||||
33 | required | TOP/raw/ | manifest.json | This file contains stain by channel details and pixel details. | |||||||||||||||||||||||
34 | required | TOP/raw/ | codebook.csv | CSV containing codebook information for the experiment. Rows are barcodes and columns are imaging rounds. The first column is the barcode target, and the following column IDs are expected to be sequential, and round identifiers are expected to be integers (not roman numerals). | |||||||||||||||||||||||
35 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | TOP/raw/ | positions.csv | file that includes the top left coordinate of each tiled image. This is required to stitch the images. | ||||||||||||||
36 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | TOP/raw/ | dataorganization.csv | necessary image definitions | ||||||||||||||
37 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | TOP/raw/ | *.DAX | The raw image stack. | ||||||||||||||
38 | see RNAseq | see RNAseq (with probes) | see RNAseq (with probes) | n/a | required | n/a | n/a | n/a | n/a | TOP/raw/fastq/ | Raw sequencing files for the experiment | ||||||||||||||||
39 | n/a | n/a | n/a | n/a | n/a | n/a | TOP/raw/fastq/oligo/ | Directory containing fastq files pertaining to oligo sequencing. | |||||||||||||||||||
40 | n/a | n/a | n/a | n/a | n/a | n/a | TOP/raw/fastq/oligo/ | *.fastq.gz | fastq | https://en.wikipedia.org/wiki/FASTQ_format | https://en.wikipedia.org/wiki/FASTQ_format | yes | Illumina | no | This is a gzip version of the fastq file. This file contains the cell barcode and unique molecular identifier (technical). | ||||||||||||
41 | n/a | n/a | n/a | required | n/a | n/a | n/a | n/a | TOP/raw/fastq/RNA/ | Directory containing fastq files pertaining to RNAseq sequencing. | |||||||||||||||||
42 | n/a | n/a | n/a | required | n/a | n/a | n/a | n/a | TOP/raw/fastq/RNA/ | *_R*.fastq.gz | fastq | https://en.wikipedia.org/wiki/FASTQ_format | https://en.wikipedia.org/wiki/FASTQ_format | no | no | This is a GZip'd version of the forward and reverse fastq files from RNAseq sequencing (R1 and R2). | |||||||||||
43 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | n/a | TOP/raw/images/FOV*/ | |||||||||||||||||
44 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | n/a | TOP/raw/images/FOV*/ | *_complete_code_cell_target_call_coord.csv | Target coordinates and counts per cell. | |||||||||||||||
45 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | n/a | TOP/raw/images/FOV*/ | *.tiff | ||||||||||||||||
46 | see histology | required | optional | optional | n/a | n/a | n/a | n/a | required | TOP/raw/images/ | Directory containing raw image files. This directory should include at least one raw file. | ||||||||||||||||
47 | optional | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/raw/images/ | *_tissue.tif or *_tissue.tiff | tiff | https://en.wikipedia.org/wiki/TIFF | yes | no | Raw microscope file for the experiment. For 10X Visium CytAssist, this would be the high resolution image produced. | ||||||||||||
48 | required | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/raw/images/ | *_fiducial.tif or *_fiducial.tiff | tiff | https://en.wikipedia.org/wiki/TIFF | This is the low resolution image from the 10X CytAssist instrument that includes the fiduciary markings. | |||||||||||||
49 | optional | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/raw/images/ | *.ndpi | NDPI | Bio-Formats | Bio-Formats | yes | Hamamatsu | no | Raw microscope file for the experiment | ||||||||||
50 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | TOP/raw/images/ | *.tif | Raw microscope file for the experiment | ||||||||||||||
51 | n/a | n/a | optional | optional | n/a | optional | optional | optional | n/a | TOP/raw/images/ | overlay.jpeg | *.jpeg | yes | NanoString | State whether an overlay image was used to guide ROI selection. If an overlay is used, then the overlay details will be provided in the protocols.io protocol. If used, this needs to be uploaded. It is not included in the OME TIFF. This can be a JPEG or TIFF file | ||||||||||||
52 | n/a | n/a | optional | optional | n/a | optional | optional | optional | n/a | TOP/raw/images/ | overlay.tiff | *.tiff | yes | NanoString | State whether an overlay image was used to guide ROI selection. If an overlay is used, then the overlay details will be provided in the protocols.io protocol. If used, this needs to be uploaded. It is not included in the OME TIFF. This can be a JPEG or TIFF file | ||||||||||||
53 | n/a | n/a | n/a | n/a | n/a | required | n/a | n/a | n/a | n/a | TOP/raw/images/ | HuBMAP_ID.jpg | jpeg | Microscope image of tissue area processed by the assay. | |||||||||||||
54 | n/a | n/a | n/a | n/a | n/a | required | n/a | n/a | n/a | n/a | TOP/raw/images/ | position.txt | text | The list of pixels that are on the tissue. [Is this meant to represent a segmentation mask?] | |||||||||||||
55 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | n/a | TOP/raw/images/ | preview_scan.png | png | ||||||||||||||
56 | n/a | n/a | n/a | n/a | required | n/a | n/a | n/a | n/a | TOP/raw/Spatial_barcodes/ | Files containing spatial barcodes and coordinates. | ||||||||||||||||
57 | n/a | n/a | n/a | n/a | required | n/a | n/a | n/a | n/a | TOP/raw/Spatial_barcodes/ | spatialBarcode_sequence.fasta | fasta | no | Deduplicated spatial barcodes. | |||||||||||||
58 | n/a | n/a | n/a | n/a | required | n/a | n/a | n/a | n/a | TOP/raw/Spatial_barcodes/ | spatialBarcode_dup.txt | tab-delimited txt | no | Duplicated spatial barcodes (different ID but same sequence). Each row contains a pair of barcodes with the same sequence. | |||||||||||||
59 | n/a | n/a | n/a | n/a | required | n/a | n/a | n/a | n/a | TOP/raw/Spatial_barcodes/ | spatialBarcode_locations.txt | tab-delimited txt | no | Spatial coordinates of each spot. | |||||||||||||
60 | required | required | required | required | required | required | required | required | required | required | TOP/lab_processed/ | Experiment files that were processed by the lab generating the data. | |||||||||||||||
61 | n/a | n/a | required | required | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/ | "Initial Dataset.xlsx" | Excel | yes | NanoString | yes | An excel spreadsheet that is downloaded from the GeoMx DSP Data Analysis Suite containing QA/QC metrics based on raw, unprocessed target counts. This file contains one row per AOI/segment and no analyses span AOI. The AOIs included in this file can come from different GeoMx runs and hence span Globus uploads. So care must be taken to make sure the appropriate AOIs are included in the file. | ||||||||||
62 | n/a | n/a | optional | required | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/ | annotations.xlsx | Excel | AOI specific annotations. This might include cell type and anatomical information. | |||||||||||||
63 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | TOP/lab_processed/ | detected_transcripts.csv | , barcode_id, global_x, global_y, global_z, x, y, fov, gene, transcript_id, cell_id | A file containing the locations of each RNA target. | |||||||||||||
64 | n/a | n/a | required | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/dcc/ | DCC files generated from fastq by the Nanostring GeoMx NGS Pipeline. | |||||||||||||||
65 | n/a | n/a | required | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/dcc/ | *.dcc | DCC | no | NanoString | GeoMx NGS Pipeline | DCC files containing target probe counts, generated from fastq by the Nanostring GeoMx NGS Pipeline. | ||||||||||
66 | see histology | required | required | required | n/a | required | required | required | required | required | TOP/lab_processed/images/ | Processed image files | |||||||||||||||
67 | required | required | required | n/a | required | required | required | required | required | TOP/lab_processed/images/ | *.ome.tiff | OME TIFF | https://docs.openmicroscopy.org/ome-model/latest/ome-tiff/ | no | no | HBM892.MDXS.293.ome.tiff | OME-TIFF files (multichannel, multi-layered) produced by the microscopy experiment. If compressed, must use loss-less compression algorithm. For Visium this stitched file should only include the single capture area relevant to the current dataset. For GeoMx there will be one OME TIFF file per slide, with each slide including multiple AOIs. See the following link for the set of fields that are required in the OME TIFF file XML header. https://docs.google.com/spreadsheets/d/1YnmdTAA0Z9MKN3OjR3Sca8pz-LNQll91wdQoRPSP6Q4/edit#gid=0 | ||||||||||
68 | required | required | required | n/a | required | required | required | required | required | TOP/lab_processed/images/ | *ome-tiff.channels.csv | CSV | https://en.wikipedia.org/wiki/Comma-separated_values | OME TIFF Channels | no | no | This file provides essential documentation pertaining to each channel of the accommpanying OME TIFF. The file should contain one row per OME TIFF channel. The required fields are detailed https://docs.google.com/spreadsheets/d/1xEJSb0xn5C5fB3k62pj1CyHNybpt4-YtvUs5SUMS44o/edit#gid=0 | ||||||||||
69 | |||||||||||||||||||||||||||
70 | |||||||||||||||||||||||||||
71 | |||||||||||||||||||||||||||
72 | n/a | n/a | EPIC | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/primary_analysis/ | Primary analysis results | |||||||||||||||||
73 | n/a | n/a | EPIC | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/primary_analysis/ | "Q3 Normalized.xlsx" | Excel | yes | NanoString | DSP Data Analysis Suite | yes | Results from initial procesing by GeoMx DSP Data Analysis Suite. The collection of datasets were normalized using Q3 normalization after target genes below the limit of quantitation (LOQ) are removed. | |||||||||||
74 | n/a | n/a | n/a | n/a | EPIC | n/a | n/a | n/a | TOP/lab_processed/alignment/ | Experiment files that were processed by the lab generating the data. | |||||||||||||||||
75 | n/a | n/a | n/a | n/a | EPIC | n/a | n/a | n/a | TOP/lab_processed/alignment/ | *.bam | bam | https://en.wikipedia.org/wiki/Binary_Alignment_Map | https://en.wikipedia.org/wiki/Binary_Alignment_Map | no | Aligned sequencing data (R2 reads) from HiFi-slide experiments against reference HG38 | ||||||||||||
76 | n/a | n/a | n/a | n/a | EPIC | n/a | n/a | n/a | TOP/lab_processed/alignment/ | SpotByGene.txt.gz | no | spot x gene expression matrix | |||||||||||||||
77 | EPIC | EPIC | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/spaceranger/ | Output from the 10X Genomics SpaceRanger pipeline | ||||||||||||||||
78 | EPIC | EPIC | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/spaceranger/ | _cmdline | txt | no | 10X Genomics | SpaceRanger | SpaceRanger | no | The actual CLI invocation of spaceranger command. | |||||||||
79 | EPIC | EPIC | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/spaceranger/ | _invocation | txt | no | 10X Genomics | SpaceRanger | SpaceRanger | no | Martian runtime specification determined from CLI invocation | |||||||||
80 | EPIC | EPIC | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/spaceranger/ | _sitecheck | txt | no | 10X Genomics | SpaceRanger | SpaceRanger | no | This contains details about the local environment within which SpaceRanger was run. | |||||||||
81 | EPIC | EPIC | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/spaceranger/ | _versions | txt | no | 10X Genomics | SpaceRanger | SpaceRanger | no | This contains the version number of both SpaceRanger and Martian that were used | |||||||||
82 | EPIC | EPIC | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/spaceranger/ | raw_feature_bc_matrix.h5 | h5 | Output Matrices | no | 10X Genomics | SpaceRanger | SpaceRanger | no | HDF5 file containing unfiltered cell x gene matrix | ||||||||
83 | EPIC | EPIC | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/spaceranger/ | filtered_feature_bc_matrix.h5 | h5 | Output Matrices | no | 10X Genomics | SpaceRanger | SpaceRanger | no | HDF5 file containing called cell x gene matrix | ||||||||
84 | EPIC | EPIC | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/spaceranger/ | metrics_summary.csv | csv | Gene Expression Metrics | no | 10X Genomics | SpaceRanger | SpaceRanger | yes | Brief reporting metrics | ||||||||
85 | EPIC | EPIC | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/spaceranger/ | molecule_info.h5 | h5 | Molecule Info | no | 10X Genomics | SpaceRanger | SpaceRanger | no | HDF5 file containing (primarily) cell-barcode/umi-barcode/read triplet counts | ||||||||
86 | EPIC | EPIC | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/spaceranger/ | possorted_genome_bam.bam | BAM | Output BAM | no | 10X Genomics | SpaceRanger | SpaceRanger | no | Aligned (and position-sorted) BAM file containing sequencing data mapped against the human genome. | ||||||||
87 | EPIC | EPIC | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/spaceranger/ | possorted_genome_bam.bam.bai | BAM index | Output BAM | no | 10X Genomics | SpaceRanger | SpaceRanger | no | Index for the aligned (and position-sorted) BAM file containing sequencing data mapped against the human genome. | ||||||||
88 | EPIC | EPIC | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/spaceranger/ | cloupe.cloupe | Loupe | Loupe Cell Browser | Loupe Cell Browser | no | 10X Genomics | SpaceRanger | SpaceRanger | no | Loupe Browser file for data visualization and analysis | |||||||
89 | EPIC | EPIC | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/spaceranger/ | web_summary.html | HTML | https://en.wikipedia.org/wiki/HTML | Output Summary | no | 10X Genomics | SpaceRanger | SpaceRanger | yes | Data summary with images, metrics, and plots that can be used for quality assessment as well as errors and warnings related to data quality | |||||||
90 | EPIC | EPIC | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/spaceranger/spatial/ | Output from the 10X Genomics SpaceRanger pipeline | ||||||||||||||||
91 | EPIC | EPIC | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/spaceranger/spatial/ | aligned_fiducials.jpg | jpeg | Output Spatial | no | 10X Genomics | SpaceRanger | SpaceRanger | JPG image containing aligned fiducials for the capture area | |||||||||
92 | EPIC | EPIC | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/spaceranger/spatial/ | detected_tissue_image.jpg | jpeg | Output Spatial | no | 10X Genomics | SpaceRanger | SpaceRanger | JPG image showing capture spots that are covered by tissue | |||||||||
93 | EPIC | EPIC | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/spaceranger/spatial/ | scalefactors_json.json | json | Output Spatial | no | 10X Genomics | SpaceRanger | SpaceRanger | Spaceranger downscales images to 2000px on the smallest side. This file contains the spot size (diameter in pixels) at full and downscaled resolutions. | |||||||||
94 | EPIC | EPIC | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/spaceranger/spatial/ | tissue_hires_image.png | png | Output Spatial | no | 10X Genomics | SpaceRanger | SpaceRanger | PNG image of aligned tissue at full/original resolution | |||||||||
95 | EPIC | EPIC | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/spaceranger/spatial/ | tissue_lowres_image.png | png | Output Spatial | no | 10X Genomics | SpaceRanger | SpaceRanger | PNG image of aligned tissue at downscaled resolution | |||||||||
96 | EPIC | EPIC | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/spaceranger/spatial/ | tissue_positions_list.csv | csv | Output Spatial | no | 10X Genomics | SpaceRanger | SpaceRanger | Spatial positions of cell barcodes | |||||||||
97 | |||||||||||||||||||||||||||
98 | |||||||||||||||||||||||||||
99 | |||||||||||||||||||||||||||
100 | |||||||||||||||||||||||||||