einarolafsson/spacr-example-import

spaCR — Import test data

The same four microscope fields written in every container format and filename convention the Import module of spaCR reads, each with its cell, nucleus and pathogen masks and the measurements of its cells. It is the data behind Load test data… on the Import screen: pick a variant, and spaCR fills the screen with it and previews the import, so you can see every file land on the well, field and channel it came from.

About 283 MB in one uncompressed archive, spacr-example-import.tar. One download covers every variant.

Where the fields come from

Wells E01 and E02, fields 9 and 10, channels 1–3 of the toxo_mito example plate plate1 (einarolafsson/toxo_mito): Toxoplasma-infected host cells, channel 1 nuclei, channel 2 host cells, channel 3 parasites.

• Images are the raw acquisition planes (16-bit, not rescaled), cut to 896 × 896 px. The window is the one that keeps the most whole cells.
• Masks are the cell, nucleus and pathogen label images of the Mask run on the same plate (einarolafsson/spacr-example-measure), cut the same way. Every object the cut went through was removed, so no mask holds half an object.
• Measurements are the Measure rows of exactly the cells left in the masks (einarolafsson/spacr-example-annotate). reference/measurements.db has them as spaCR wrote them (cell, nucleus, pathogen and cytoplasm tables); each variant's measurements.db has the cell table the way a collaborator's table would arrive: spaCR's own key columns removed, and an image column naming that variant's own file.

Channels are named DAPI, FITC and TRITC in the conventions that name channels rather than number them. Import numbers named channels in sorted order, and these three sort in channel order.

The variants

variants/<key>/plate1/ holds the images, variants/<key>/masks/{cell,nucleus,pathogen}/ the masks named the same way, and variants/<key>/measurements.db the table.

Key	Button	Files	Naming (metadata_type)	Example
zeiss_czi	Test Zeiss CZI import	Zeiss CZI, one plane per file	zeiss_zen_split_tiles	E01/plate1_S00001_T00009_C00001.czi
cellvoyager	Test Yokogawa CellVoyager import	TIFF	cellvoyager	plate1_E01_T0001F009L01A01Z01C01.tif
cq1	Test Yokogawa CQ1 import	TIFF	cq1	W0097F0009T0001Z000C1.tif
opera_phenix	Test Opera Phenix import	TIFF	opera_phenix	Images/r05c01f09p01-ch1sk1fk1fl1.tiff
imagexpress	Test ImageXpress import	TIFF	imagexpress	TimePoint_1/plate1_E01_s9_w1<GUID>.TIF
arrayscan	Test ArrayScan import	TIFF	arrayscan	plate1_E01f08d0.TIF
arrayscan_kinetic	Test ArrayScan kinetic import	TIFF	arrayscan_kinetic	plate1i3t001E01f08d0.TIF
evos	Test EVOS import	TIFF	evos	scan_R_p1_z1_0_E01f09d0.tif
incell	Test IN Cell import	TIFF	incell	E - 01(fld 9 wv DAPI - DAPI).tif
scanr	Test ScanR import	TIFF	scanr	data/E1--W00097--P00009--Z00000--T00000--DAPI.tif
cytation	Test Cytation import	TIFF	cytation	E1_01_1_9_DAPI_001.tif
leica_matrix_screener	Test Leica Matrix Screener import	OME-TIFF, one plane per file	leica_matrix_screener	slide--S00/chamber--U00--V04/field--X08--Y00/image--L00--S00--U00--V04--J20--E00--O00--X08--Y00--T00--Z00--C00.ome.tif
leica_lasx_series	Test Leica LAS X series import	TIFF	leica_lasx_series	E01/Series009_z00_ch00.tif
leica_lasx_series_time	Test Leica LAS X timelapse import	TIFF	leica_lasx_series_time	E01/Pos008_t000_z00_ch00.tif
nikon_nis_xy	Test Nikon NIS-Elements import	TIFF	nikon_nis_xy	E01xy09c1.tif
nikon_jobs	Test Nikon JOBS import	TIFF	nikon_jobs	WellE01_ChannelDAPI_Seq0009.tif
micromanager_mda	Test Micro-Manager import	TIFF	micromanager_mda	E01/img_channel000_position008_time000000000_z000.tif
zeiss_zen_split_tiles	Test Zeiss ZEN split tiles import	TIFF	zeiss_zen_split_tiles	E01/plate1_S00001_T00009_C00001.tiff
custom	Test custom naming import	TIFF	custom (?P<plateID>[^_]+)__(?P<wellID>[A-Z]\d{2})__site(?P<fieldID>\d+)__(?P<chanID>[A-Za-z0-9]+)	toxo-plate1__E01__site09__DAPI.tif
auto	Test folder-layout import	TIFF	auto	E01/fov09_ch1.tif
ome_tiff	Test OME-TIFF import	OME-TIFF, three channels per file	auto	E01/field009.ome.tif
tiff_stack	Test TIFF stack import	ImageJ TIFF stack, three channels per file	auto	E01/field009.tif
nikon_nd2	Test Nikon ND2 import	Nikon ND2 (public sample)	auto	A01/WellA01_ChannelBF_Seq0001.nd2
leica_lif	Test Leica LIF import	Leica LIF (public samples)	auto	A01/FRAP.lif

What is true of every file: manifest.csv

One row per file. path is relative to the unpacked import_example/ folder; well, field, channel, z and t are what the file truly is, and source_field is the field number on the original plate. field_identity says what an import should recover: number means the field number itself (field 9 stays field 9); rank means the order within the well, for the variants whose names carry no field number (a folder layout, a Leica Matrix Screener X/Y position, a file of channels). The manifest is the last member of the archive, so a download that died part-way has none and reads as absent.

Verified

Every variant was imported with spaCR's own planner and each output plane compared with the manifest: well, field, channel, z and t, every mask paired with its field, and every measurement row matched to an object in the masks.

Variant	Result
zeiss_czi	passed
cellvoyager	passed
cq1	passed
opera_phenix	passed
imagexpress	passed
arrayscan	passed
arrayscan_kinetic	passed
evos	passed
incell	passed
scanr	passed
cytation	passed
leica_matrix_screener	passed
leica_lasx_series	passed
leica_lasx_series_time	passed
nikon_nis_xy	passed
nikon_jobs	passed
micromanager_mda	passed
zeiss_zen_split_tiles	passed
custom	passed
auto	passed
ome_tiff	passed
tiff_stack	passed
nikon_nd2	passed
leica_lif	passed

What a pass proves, and what it does not: the files were written to follow each convention as spaCR's convention table documents it (the same table Mask uses, including which numbers count from zero), and read back by the Import module. It shows Import inverts those conventions. It cannot show that the table is right about every instrument; conventions marked provisional in spaCR's Naming list are the ones built from few real examples.

ND2 and LIF

No open library writes Nikon ND2 or Leica LIF, so those two variants are not these fields: they are public sample files from downloads.openmicroscopy.org, redistributed under their licence, CC BY 4.0 (the text is in each folder as LICENSE-CC-BY-4.0.txt). They carry no masks, so their buttons fill the Format Converter rather than the Import screen.

• variants/nikon_nd2/plate1/A01/WellA01_ChannelBF_Seq0001.nd2 — https://downloads.openmicroscopy.org/images/ND2/maxime/BF007.nd2 -- (c) Maxime Woringer, CC BY 4.0
• variants/leica_lif/plate1/A01/FRAP.lif — https://downloads.openmicroscopy.org/images/Leica-LIF/seanwarren/150519_FRAP_test_ROIs_chromagreen/150519_FRAP_test_ROIs_chromagreen.lif -- (c) Sean Warren, CC BY 4.0
• variants/leica_lif/plate1/A01/PR2729_frameOrderCombinedScanTypes.lif — https://downloads.openmicroscopy.org/images/Leica-LIF/michael/PR2729_frameOrderCombinedScanTypes.lif -- (c) Michael Goelzer, CC BY 4.0

Using it

In spaCR, open Import and press Load test data…. The first choice downloads the archive into ~/.cache/spacr/example_data/plate1/import_example/; later choices open from there. From a terminal: spacr-download import.

Licence

MIT, like spaCR's other example sets, except the two sample folders variants/nikon_nd2 and variants/leica_lif, which are CC BY 4.0 by the authors named above.