| A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | AA | AB | AC | AD | AE | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | Directory Structure Schema: | https://docs.google.com/spreadsheets/d/1fDxpEvln9o7P0YrTZPBxpTY98UkDuWEhmaMUFA8LNHE/edit#gid=1843407110 | ||||||||||||||||||||
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5 | Options: required, optional, EPIC, n/a | Path | File name | is QA? | Example | File or directory description | ||||||||||||||||
6 | Seq-Scope | Stereo-Seq | Visium (no probes) | Visium (with probes) | Visium HD | Illumina Spatial Technology | GeoMx (NGS) | GeoMx (nCounter) | HiFi | hrsTP-seq (DBiTSeq) | Xenium | Resolve | CosMx Transcriptomics | CosMx Proteomics | MERFISH | |||||||
7 | required | required | required | required | required | required | required | required | required | required | required | required | required | required | required | TOP/ | Top level directory | |||||
8 | optional | required RNAseq | required RNAseq (with probes) | required RNAseq (with probes) | n/a | required RNAseq (with probes) | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | Sequencing Files To Be Included | |||||||
9 | optional | required | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | Histology Files To Be Included | |||||||
10 | required | required | see histology | required | required | required | required | required | required | required | required | required | required | required | required | TOP/extras/ | Folder for general lab-specific files related to the dataset | |||||
11 | n/a | required | required | required | required | required | required | required | required | required | required | required | required | required | TOP/extras/ | microscope_hardware.json | 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. | ||||
12 | n/a | n/a | optional | optional | optional | optional | optional | optional | optional | optional | optional | optional | optional | optional | TOP/extras/ | microscope_settings.json | 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. | ||||
13 | required | n/a | required | required | required | required | required | required | required | required | required | required | required | required | required | TOP/raw/ | All raw data files for the experiment. | |||||
14 | n/a | n/a | required | required | required | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/raw/ | <slide ID>.[gpr | vlf] | 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. Depending upon the version of Visum and the web form being used, one of these file types might not be available. | |||
15 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | required | n/a | TOP/raw/ | *_exprMat_file.csv | Cell expression matrix with raw counts of genes for each identified cell. Apart from the gene specific columns, additional columns include: - the origin of the cell (fov, unique cell id) - negative probes - probes associated with the fiducial frame (SystemControl) | ||||
16 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | required | n/a | TOP/raw/ | *_fov_positions_file.csv | FOV Positions file that provides an overview of the tissue locations and to help specify separate regions and/or tissues on the slide. This contains information about: - Slide – slide number it comes from - FOV – filed of view - X_mm/Y_mm – x/y coordinates of FOV positions in mm (previously in px) | ||||
17 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | optional | optional | n/a | TOP/raw/ | latest.fovs.csv | Legacy version of file located in the RunSummary directory of AtoMx exports that is distinct from the *fov_positions_file.csv and include Z-axis and Z-offset information. | ||||
18 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | optional | optional | n/a | TOP/raw/ | FOV_locations.csv | Current version of file located in the RunSummary directory of AtoMx exports that is distinct from the *fov_positions_file.csv and include Z-axis and Z-offset information. | ||||
19 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | required | n/a | TOP/raw/ | *_metadata_file.csv | Cell metadata file containing the following information: - the origin of the cell (fov, unique cell id) - physical properties of the cell (area, aspect ratio, width, height) - location of the cell centroid within each FOV (center X/Y local) and global position (center X/Y global) - information about the protein staining (min/max intensity) - the type of protein my be specific to each experiment, but generally includes: DAPI, Membrane, PanCK, CD45 - other (e.g. Seurat information if that pipeline was used within AtoMx, some data quality information) | ||||
20 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | n/a | n/a | TOP/raw/ | *_tx_file.csv | File containing specific transcript location output with information regarding all transcripts detected across various fields of view (FOVs), including cell_ID, global and local coordinates, Z-slice index, target and the subcellular compartment in which the transcript was identified. | ||||
21 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | n/a | TOP/raw/ | *polygons.csv | File containing the coordinate data for the polygons outlining the boundaries of every cell identified during the imaging process. | ||||
22 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | n/a | TOP/raw/ | plex*.txt | File containing ProbeID-to-DisplayName keys. | ||||
23 | n/a | n/a | n/a | n/a | n/a | n/a | required | required | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/raw/ | *_LabWorksheet.txt | 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. | ||||
24 | n/a | n/a | n/a | n/a | n/a | n/a | required | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/raw/ | *_config.ini | Needed to generate the DCC file from the fastq file. Contains pipeline processing parameters. Generated by DSP run, prior to sequencing. | ||||
25 | n/a | n/a | n/a | n/a | n/a | n/a | optional | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/raw/ | *_SeqCodeIndices.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. | ||||
26 | n/a | n/a | n/a | n/a | n/a | n/a | optional | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/raw/ | *_SampleSheet.csv | Used by NextSeq 1000/2000 users, along with whitelist.txt, in place of SeqCodeIndices.csv | ||||
27 | n/a | n/a | n/a | n/a | n/a | n/a | optional | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/raw/ | *_whitelist.txt | Used by NextSeq 1000/2000 users, along with SampleSheet.csv, in place of SeqCodeIndices.csv | ||||
28 | n/a | n/a | n/a | n/a | n/a | n/a | optional | optional | n/a | optional | optional | required | required | n/a | TOP/raw/ | markers.csv | A csv file describing any morphology markers used to guide ROI and/or AOI selection. This should minimally contain name of fluorophor, vendor, channel. | |||||
29 | n/a | n/a | n/a | n/a | n/a | n/a | required | required | n/a | n/a | n/a | n/a | n/a | n/a | TOP/raw/ | *.pkc | The file listing probe barcode sequence and corresponding gene symbol and, if appropriate, proteins targeted by that probe. This should be consistent for the same probe panel. | |||||
30 | n/a | n/a | n/a | see RNAseq (with probes) | see RNAseq (with probes) | n/a | see RNAseq (with probes) | optional | n/a | optional | optional | optional | optional | optional | TOP/raw/ | additional_panels_used.csv | 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. | |||||
31 | n/a | n/a | n/a | n/a | n/a | n/a | required | required | n/a | required | TOP/raw/ | gene_panel.csv | The list of target genes. The expected format is: ensembl ID, gene_name. If multiple ensemble IDs per gene name, a comma separated list of ensembl ID can be used. | |||||||||
32 | n/a | n/a | n/a | n/a | n/a | n/a | optional | optional | optional | optional | optional | TOP/raw/ | custom_probe_set.csv | 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). | ||||||||
33 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | optional | n/a | n/a | n/a | n/a | TOP/raw/ | custom_probe_set.bed | This is a BED file version of the custom probe set file. | ||||
34 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | required | optional | n/a | n/a | TOP/raw/ | transcript_locations.csv | Contains decription of the location of all decoded transcripts. 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. | |||||
35 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | optional | required | optional | n/a | n/a | TOP/raw/ | custom_gene_list.csv | This describes the target genes profiled by the assay. For advanced design, this can be probes sequences for splicing or other analysis for any target of interest. The format should minimally contain: gene name, ensemble ID | |||||
36 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | optional | optional | optional | n/a | n/a | TOP/raw/ | probes.csv | A CSV file describing the probe panel used. This is typically what's used to specific the probe set when ordering a probe panel for a Xenium run. | |||||
37 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | n/a | n/a | n/a | n/a | TOP/raw/ | gene_panel.json | This is the JSON file describing the probes, as output from the xenium-ranger pipeline. | ||||
38 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | optional | n/a | n/a | n/a | n/a | TOP/raw/ | protein_panel.json | This is the JSON file describing the protein targets, as output from the xenium-ranger pipeline. | ||||
39 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | n/a | 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. | ||||
40 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | n/a | n/a | n/a | n/a | n/a | n/a | TOP/raw/ | *.cdf | Cartridge definition file for the nCounter. | |||||
41 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | optional | TOP/raw/ | micron_to_mosaic_pixel_transform.csv | Matrix used to transform from pixels to physical distance. | ||||
42 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | optional | TOP/raw/ | manifest.json | This file contains stain by channel details and pixel details. | ||||
43 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | 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). | ||||
44 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | optional | TOP/raw/ | positions.csv | File that includes the top left coordinate of each tiled image. This is required to stitch the images. | ||||
45 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | optional | TOP/raw/ | dataorganization.csv | Necessary image definitions | ||||
46 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | optional | TOP/raw/data/ | All raw stack data files for the MERFISH experiment. | |||||
47 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | optional | TOP/raw/data/ | *.dax | The raw image stack for MERFISH v1 | ||||
48 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | optional | TOP/raw/data/ | *.inf | Information file with dax image format specifications for MERFISH v1. Variable expected for downstream processing with PIPEFISH are: frame dimensions, number of frames, little/big endian, stage X and Y locations, lock target, scalemin, and scalemax. | ||||
49 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | optional | TOP/raw/data/ | *.zip | The raw image stack for MERFISH v2 | ||||
50 | n/a | n/a | see RNAseq | see RNAseq (with probes) | see RNAseq (with probes) | n/a | see RNAseq (with probes) | n/a | required | n/a | n/a | n/a | n/a | n/a | TOP/raw/fastq/ | Raw sequencing files for the experiment | ||||||
51 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/raw/fastq/oligo/ | Directory containing fastq files pertaining to oligo sequencing. | |||||||||||
52 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/raw/fastq/oligo/ | *.fastq.gz | no | This is a gzip version of the fastq file. This file contains the cell barcode and unique molecular identifier (technical). | |||||||||
53 | n/a | n/a | n/a | required | n/a | n/a | n/a | n/a | n/a | TOP/raw/fastq/RNA/ | Directory containing fastq files pertaining to RNAseq sequencing. | |||||||||||
54 | n/a | n/a | n/a | required | n/a | n/a | n/a | n/a | n/a | TOP/raw/fastq/RNA/ | *_R*.fastq.gz | no | This is a GZip'd version of the forward and reverse fastq files from RNAseq sequencing (R1 and R2). | |||||||||
55 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | required | n/a | TOP/raw/images/FOV*/ | Directory containing imaging tiles. | ||||||
56 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | n/a | n/a | TOP/raw/images/FOV*/ | *_complete_code_cell_target_call_coord.csv | Target coordinates and counts per cell. | |||||
57 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | required | n/a | TOP/raw/images/FOV*/ | *.tiff or *.tif | The morphology marker multi-channel TIFF or TIF file. | |||||
58 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | n/a | TOP/raw/images/FOV*/ProteinImages/ | *.tiff | High-resolution, multi-layered images generated by the CosMx Spatial Molecular Imager (SMI) that contain the spatial data for up to 76 different proteins imaged at single-cell and subcellular resolution within a tissue sample | |||||
59 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | n/a | TOP/raw/images/FOV*/ProteinMasks/ | *.tiff | High-resolution image file that shows the segmentation of cells within a tissue sample, based on the protein staining data generated by the Bruker CosMx Spatial Molecular Imager. This mask file outlines the boundaries of individual cells and is used to accurately identify and analyze protein expression at the single-cell level. | |||||
60 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | optional | optional | n/a | TOP/raw/images/FOV*/ | overlay.jpeg | 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. | ||||
61 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | optional | optional | n/a | TOP/raw/images/FOV*/ | overlay.[tif | tiff] | 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, TIF or TIFF file | ||||
62 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | optional | optional | TOP/raw/images/FOV*/ | CellOverlay_FOV*.jpg | File depicting a visual overlay of key spatial transcriptomics data for the specific field of view (FOV). These images combine cellular morphology with transcript information to provide context for the gene expression data. | |||||
63 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | optional | optional | TOP/raw/images/FOV*/ | CellLabels_F*.[tif | tiff] | A TIFF or TIF image containing the results of cell segmentation. It provides a visual map of the identified cells, with each cell in a field of view (FOV) assigned a unique numerical label. | |||||
64 | n/a | n/a | see histology | required | required | n/a | optional | optional | n/a | n/a | 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. | |||||
65 | n/a | n/a | optional | optional | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/raw/images/ | *_tissue.tif or *_tissue.tiff | no | Raw microscope file for the experiment. For 10X Visium CytAssist, this would be the high resolution image produced. | ||||
66 | n/a | n/a | required | required | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/raw/images/ | *_fiducial.tif or *_fiducial.tiff | This is the low resolution image from the 10X CytAssist instrument that includes the fiduciary markings. | |||||
67 | n/a | n/a | optional | optional | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/raw/images/ | *.ndpi | no | Raw microscope file for the experiment | ||||
68 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | optional | TOP/raw/images/ | *.tif | Raw microscope file for the experiment in MERFISH v.1 | ||||
69 | n/a | n/a | n/a | n/a | n/a | n/a | optional | optional | n/a | n/a | optional | optional | n/a | n/a | n/a | TOP/raw/images/ | overlay.jpeg | 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. | ||||
70 | n/a | n/a | n/a | n/a | n/a | n/a | optional | optional | n/a | n/a | optional | optional | n/a | n/a | n/a | TOP/raw/images/ | overlay.tiff | 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, TIF or TIFF file | ||||
71 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | n/a | n/a | n/a | n/a | n/a | TOP/raw/images/ | HuBMAP_ID.jpg | Microscope image of tissue area processed by the assay. | ||||
72 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | n/a | n/a | n/a | n/a | n/a | TOP/raw/images/ | position.txt | The list of pixels that are on the tissue. [Is this meant to represent a segmentation mask?] | ||||
73 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | required | n/a | TOP/raw/images/ | preview_scan.png | Assists in selection of regions of FOVs using the grid FOV placement tool. This is typically downloaded from the AtoMx server. A screen shot during the FOV selection process would also suffice. | ||||
74 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | n/a | n/a | n/a | n/a | n/a | TOP/raw/Spatial_barcodes/ | Files containing spatial barcodes and coordinates. | ||||||
75 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | n/a | n/a | n/a | n/a | n/a | TOP/raw/Spatial_barcodes/ | spatialBarcode_sequence.fasta | Deduplicated spatial barcodes. | |||||
76 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | n/a | n/a | n/a | n/a | n/a | TOP/raw/Spatial_barcodes/ | spatialBarcode_dup.txt | Duplicated spatial barcodes (different ID but same sequence). Each row contains a pair of barcodes with the same sequence. | |||||
77 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | n/a | n/a | n/a | n/a | n/a | TOP/raw/Spatial_barcodes/ | spatialBarcode_locations.txt | Spatial coordinates of each spot. | |||||
78 | required | required | required | required | required | required | required | required | required | required | required | required | n/a | required | required | TOP/lab_processed/ | Experiment files that were processed by the lab generating the data. | |||||
79 | n/a | required | required | required | required | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/ | alignment.json | JSON file for the manual tissue alignment created using Loupe browser and used as input to Space Ranger. | |||||
80 | n/a | n/a | n/a | n/a | n/a | required | required | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/ | "Initial Dataset.xlsx" | 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. | ||||
81 | n/a | n/a | n/a | n/a | n/a | optional | required | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/ | annotations.xlsx | AOI specific annotations. This might include cell type and anatomical information. | |||||
82 | required | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/ | barcodes.tsv.gz | ||||||
83 | optional | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/ | barcodes.minmax.tsv | Can be derived from barcodes.tsv.gz | |||||
84 | required | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/ | features.tsv.gz | ||||||
85 | required | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/ | matrix.mtx.gz | ||||||
86 | n/a | n/a | n/a | n/a | n/a | required | n/a | 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. | ||||||
87 | n/a | n/a | n/a | n/a | n/a | required | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/dcc/ | *.dcc | DCC files containing target probe counts, generated from fastq by the Nanostring GeoMx NGS Pipeline. | |||||
88 | required | see histology | required | required | required | required | required | n/a | required | required | required | n/a | optional | optional | TOP/lab_processed/images/ | Processed image files | ||||||
89 | n/a | required | required | required | required | required | n/a | required | required | required | n/a | n/a | optional | TOP/lab_processed/images/ | *.ome.tiff | 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 | ||||
90 | n/a | required | required | required | required | n/a | n/a | required | required | required | n/a | n/a | optional | TOP/lab_processed/images/ | *ome-tiff.channels.csv | 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 | |||||
91 | n/a | optional | optional | optional | n/a | optional | n/a | n/a | n/a | optional | n/a | optional | optional | optional | TOP/lab_processed/images/ | *tissue-boundary.geojson | yes | If the boundaries of the tissue have been identified (e.g., by manual efforts), then the boundary geometry can be included as a GeoJSON file named “*.tissue-boundary.geojson”. | ||||
92 | optional | optional | optional | n/a | optional | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/transformations/ | This directory contains transformation matrices that capture how each modality is aligned with the other and can be used to visualize overlays of multimodal data. This is needed to overlay images from the exact same tissue section (e.g., MALDI imaging mass spec, autofluorescence microscopy, MxIF, histological stains). In these cases data type may have different pixel sizes and slightly different orientations (i.e., one may be rotated relative to another). | ||||||||||
93 | optional | optional | optional | n/a | optional | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/transformations/ | *.txt | no | Transformation matrices used to overlay images from the exact same tissue section (e.g., MALDI imaging mass spec, autofluorescence microscopy, MxIF, histological stains). | ||||||||
94 | n/a | n/a | n/a | n/a | required | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/primary_analysis/ | Primary analysis results | ||||||||
95 | n/a | n/a | n/a | n/a | optional | n/a | n/a | n/a | n/a | n/a | n/a | n/a | TOP/lab_processed/primary_analysis/ | *.xlsx | yes | File containing results from initial processing by GeoMx DSP Data Analysis Suite including optional removal of segments and targets based on QC flags and LOQ and normalization using Q3 normalization. This file will not be available for sites that do not use the GeoMx DSP Data Analysis Suite. | ||||||
96 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | TOP/lab_processed/merfish_output/ | Directory containing the MERFISH cell x gene analysis. | |||||
97 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | required | TOP/lab_processed/merfish_output/ | detected_transcripts.csv | File containing a list of detected transcripts in sample. Transcripts are stored as a list with the following associated metadata. barcode_id, global_x, global_y, global_z, x, y, fov, transcript_score, gene, transcript_id, cell_id | ||||
98 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | optional | TOP/lab_processed/merfish_output/ | detected_transcripts.parquet | File containing a list of detected transcripts in sample. Transcripts are stored as a list with x, y, and z locations in the sample. | ||||
99 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | optional | TOP/lab_processed/merfish_output/images/ | Directory containing the MERFISH mosaic image files. | |||||
100 | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | n/a | optional | TOP/lab_processed/merfish_output/images/ | mosaic_.*.tif | File containing a stitched mosaic of whole sample. Mosaic tif files are downsampled from high resolution raw imaging data. | ||||