Datasets:

einarolafsson
/

spacr-example-dose

plate stringclasses 4 values	well stringlengths 3 3	compound stringclasses 59 values	moa stringclasses 51 values	dose_uM float64 0 20	Cells_Number_Object_Number float64 3.5 193	Cells_AreaShape_Area float64 6.4k 33.1k	Nuclei_AreaShape_Area float64 2.19k 6.03k	Cells_AreaShape_FormFactor float64 0.17 0.46	Cells_Intensity_MeanIntensity_DNA float64 0.01 0.04	Cells_Intensity_MeanIntensity_Mito float64 0.01 0.07	Cells_Intensity_MeanIntensity_ER float64 0.03 0.09	Cells_Intensity_MeanIntensity_RNA float64 0.01 0.02	Cells_Intensity_MeanIntensity_AGP float64 0.03 0.07	Nuclei_Intensity_IntegratedIntensity_DNA float64 40.4 366	Cytoplasm_Granularity_1_Mito float64 13.4 62.1
SQ00014812	A01	DMSO	null	0	114	11,598	2,875	0.32062	0.020528	0.009889	0.040988	0.012837	0.038885	157.28	55.823
SQ00014812	A02	DMSO	null	0	127	11,342	2,800.5	0.3239	0.017427	0.008989	0.039771	0.014324	0.036	130.4	55.316
SQ00014812	A03	DMSO	null	0	147	10,228	2,691	0.33727	0.019639	0.00942	0.041316	0.014548	0.035815	136.32	54.462
SQ00014812	A04	DMSO	null	0	156	9,827	2,670	0.33836	0.020216	0.008874	0.043115	0.015199	0.037806	132.29	54.716
SQ00014812	A05	DMSO	null	0	163	9,300	2,650	0.34067	0.017078	0.009303	0.045304	0.015226	0.033683	102.17	53.66
SQ00014812	A06	DMSO	null	0	150	10,272	2,654	0.33298	0.016124	0.009271	0.045194	0.01484	0.033472	103.88	54.439
SQ00014812	A07	aclidinium	acetylcholine receptor antagonist	10	165	9,213	2,654	0.348	0.017846	0.009899	0.048294	0.016677	0.034717	108.33	54.004
SQ00014812	A08	aclidinium	acetylcholine receptor antagonist	3.3333	145	10,546	2,666	0.33304	0.019579	0.008685	0.041331	0.01479	0.036256	137.55	55.25
SQ00014812	A09	aclidinium	acetylcholine receptor antagonist	1.1111	153	10,007	2,634	0.33671	0.019967	0.008522	0.043275	0.015093	0.038515	129.69	55.351
SQ00014812	A10	aclidinium	acetylcholine receptor antagonist	0.3704	162	9,354.5	2,560.5	0.34558	0.020502	0.008706	0.044408	0.01546	0.038032	129.44	55.999
SQ00014812	A11	aclidinium	acetylcholine receptor antagonist	0.1235	141	9,893.5	2,596	0.33991	0.018613	0.008359	0.042866	0.014378	0.037689	121.7	56.536
SQ00014812	A12	aclidinium	acetylcholine receptor antagonist	0.0412	153	9,283	2,594	0.33801	0.019817	0.008292	0.043328	0.014724	0.038108	122.29	56.717
SQ00014812	A13	pitavastatin	HMGCR inhibitor	10	28	7,966	2,910	0.37061	0.023329	0.016251	0.07376	0.019172	0.059609	136.78	38.858
SQ00014812	A14	pitavastatin	HMGCR inhibitor	3.3333	118	9,305	2,533	0.36943	0.021145	0.009999	0.051218	0.016064	0.04556	129.75	49.808
SQ00014812	A15	pitavastatin	HMGCR inhibitor	1.1111	143	9,665.5	2,515.5	0.34643	0.020481	0.008621	0.043175	0.014416	0.039536	131.17	55.166
SQ00014812	A16	pitavastatin	HMGCR inhibitor	0.3704	143.5	10,024	2,562	0.32935	0.019939	0.008491	0.041367	0.013766	0.038379	130	54.368
SQ00014812	A17	pitavastatin	HMGCR inhibitor	0.1235	151	9,746	2,678	0.33645	0.020881	0.008444	0.042366	0.014132	0.038357	132.81	54.995
SQ00014812	A18	pitavastatin	HMGCR inhibitor	0.0412	148	9,666	2,588	0.32698	0.019607	0.008295	0.041296	0.013415	0.036392	125.79	55.685
SQ00014812	A19	entinostat	HDAC inhibitor	10	45	13,896	2,900	0.26169	0.017256	0.011684	0.045719	0.013666	0.047333	152.43	42.207
SQ00014812	A20	entinostat	HDAC inhibitor	3.3333	83	14,096	2,584.5	0.25244	0.016152	0.010138	0.041264	0.012564	0.038845	137.65	47.164
SQ00014812	A21	entinostat	HDAC inhibitor	1.1111	106	12,222	2,586	0.27912	0.015132	0.009535	0.044081	0.012888	0.033891	109.17	50.493
SQ00014812	A22	entinostat	HDAC inhibitor	0.3704	128	11,155	2,580	0.30185	0.014406	0.009492	0.04646	0.013876	0.033224	92.947	53.326
SQ00014812	A23	entinostat	HDAC inhibitor	0.1235	128	10,854	2,629	0.30518	0.017265	0.009043	0.039843	0.012021	0.033723	116.98	54.523
SQ00014812	A24	entinostat	HDAC inhibitor	0.0412	136	10,579	2,651	0.30397	0.018765	0.008892	0.038097	0.011522	0.03427	129.35	53.926
SQ00014812	B01	DMSO	null	0	152	9,822	2,659	0.33533	0.019773	0.010163	0.044129	0.015702	0.038701	132.88	52.168
SQ00014812	B02	DMSO	null	0	137	10,266	2,664	0.33576	0.019672	0.010855	0.042536	0.015395	0.037748	138.48	51.991
SQ00014812	B03	DMSO	null	0	135	10,726	2,778	0.33786	0.020003	0.010959	0.041912	0.015018	0.036015	142.69	52.752
SQ00014812	B04	DMSO	null	0	146	10,034	2,608.5	0.34026	0.020284	0.01123	0.042922	0.015454	0.036449	141.18	49.998
SQ00014812	B05	DMSO	null	0	155	9,846	2,640	0.34961	0.021169	0.01078	0.043355	0.01551	0.03711	142.32	53.106
SQ00014812	B06	DMSO	null	0	150	10,442	2,603	0.33442	0.020615	0.010772	0.042598	0.015228	0.036552	140.92	51.672
SQ00014812	B07	gatifloxacin	bacterial DNA gyrase inhibitor	10	150	9,575	2,645	0.33873	0.021859	0.010868	0.044865	0.016103	0.037445	144.05	51.268
SQ00014812	B08	gatifloxacin	bacterial DNA gyrase inhibitor	3.3333	150	10,309	2,654.5	0.33608	0.020359	0.010735	0.042697	0.015303	0.036775	140.5	51.785
SQ00014812	B09	gatifloxacin	bacterial DNA gyrase inhibitor	1.1111	157	9,661.5	2,563.5	0.33937	0.020974	0.010609	0.045687	0.016176	0.03936	135.3	51.894
SQ00014812	B10	gatifloxacin	bacterial DNA gyrase inhibitor	0.3704	174	8,833	2,557	0.34661	0.02217	0.010488	0.047002	0.016652	0.039991	132.11	51.932
SQ00014812	B11	gatifloxacin	bacterial DNA gyrase inhibitor	0.1235	161	9,575	2,551	0.34201	0.020175	0.010014	0.045019	0.015456	0.039155	128.04	53.451
SQ00014812	B12	gatifloxacin	bacterial DNA gyrase inhibitor	0.0412	170	8,978	2,553	0.34064	0.020801	0.010057	0.045468	0.015624	0.039651	125	53.257
SQ00014812	B13	CP-724714	EGFR inhibitor\|protein tyrosine kinase inhibitor	10	92	11,852	2,681.5	0.32894	0.017888	0.010124	0.041212	0.013297	0.038479	131.92	52.712
SQ00014812	B14	CP-724714	EGFR inhibitor\|protein tyrosine kinase inhibitor	3.3333	121	11,232	2,571	0.32044	0.018254	0.009684	0.04005	0.013263	0.036819	128.34	54.915
SQ00014812	B15	CP-724714	EGFR inhibitor\|protein tyrosine kinase inhibitor	1.1111	150	10,152	2,575	0.33306	0.019466	0.010268	0.040737	0.01385	0.036341	130.58	53.106
SQ00014812	B16	CP-724714	EGFR inhibitor\|protein tyrosine kinase inhibitor	0.3704	161	9,171	2,525	0.33695	0.021007	0.010016	0.041716	0.01449	0.038014	131.29	52.447
SQ00014812	B17	CP-724714	EGFR inhibitor\|protein tyrosine kinase inhibitor	0.1235	159	9,766.5	2,605	0.33359	0.020392	0.010161	0.041975	0.014163	0.036177	129.44	52.047
SQ00014812	B18	CP-724714	EGFR inhibitor\|protein tyrosine kinase inhibitor	0.0412	155	9,354.5	2,572.5	0.33694	0.020935	0.010401	0.041542	0.014626	0.037278	132.45	52.779
SQ00014812	B19	decitabine	DNA methyltransferase inhibitor	10	102	13,374	3,054	0.28519	0.018738	0.009867	0.038006	0.012469	0.0358	153.81	49.524
SQ00014812	B20	decitabine	DNA methyltransferase inhibitor	3.3333	98	13,481	3,032	0.27334	0.015753	0.009699	0.040926	0.012418	0.034456	121.61	51.145
SQ00014812	B21	decitabine	DNA methyltransferase inhibitor	1.1111	114	12,255	2,825	0.29235	0.017174	0.009687	0.037488	0.012285	0.033528	130.24	51.484
SQ00014812	B22	decitabine	DNA methyltransferase inhibitor	0.3704	134	10,679	2,808	0.31455	0.018445	0.009473	0.041163	0.013745	0.035069	126.38	52.939
SQ00014812	B23	decitabine	DNA methyltransferase inhibitor	0.1235	129	11,024	2,791	0.30612	0.017195	0.00882	0.039025	0.01273	0.033741	119.4	53.84
SQ00014812	B24	decitabine	DNA methyltransferase inhibitor	0.0412	139	10,301	2,729	0.31209	0.018465	0.008498	0.03986	0.012966	0.034584	126	53.416
SQ00014812	C01	CGS-20625	benzodiazepine receptor agonist\|GABA benzodiazepine site receptor partial agonist	10	128	10,468	2,591	0.34494	0.017887	0.008993	0.043016	0.017719	0.038081	126.08	53.889
SQ00014812	C02	CGS-20625	benzodiazepine receptor agonist\|GABA benzodiazepine site receptor partial agonist	3.3333	142.5	10,219	2,567	0.35028	0.018279	0.009737	0.04296	0.017705	0.038099	126.81	52.731
SQ00014812	C03	CGS-20625	benzodiazepine receptor agonist\|GABA benzodiazepine site receptor partial agonist	1.1111	151	9,908	2,620	0.35016	0.019716	0.009079	0.043256	0.018116	0.037071	133.32	55.452
SQ00014812	C04	CGS-20625	benzodiazepine receptor agonist\|GABA benzodiazepine site receptor partial agonist	0.3704	163	9,403	2,656	0.35331	0.021017	0.009513	0.044323	0.018386	0.037837	135.11	55.377
SQ00014812	C05	CGS-20625	benzodiazepine receptor agonist\|GABA benzodiazepine site receptor partial agonist	0.1235	163	9,514	2,523	0.3547	0.020035	0.00918	0.043081	0.01752	0.037478	132.93	54.725
SQ00014812	C06	CGS-20625	benzodiazepine receptor agonist\|GABA benzodiazepine site receptor partial agonist	0.0412	160	9,382	2,524	0.35336	0.019971	0.009466	0.044237	0.017929	0.037413	131.34	53.585
SQ00014812	C07	epothilone-B	microtubule stabilizing agent\|tubulin polymerization inhibitor	10	32	23,106	4,764	0.27785	0.015621	0.012543	0.040833	0.015453	0.037541	249.09	43.48
SQ00014812	C08	epothilone-B	microtubule stabilizing agent\|tubulin polymerization inhibitor	3.3333	30	24,903	5,036	0.26663	0.015006	0.01245	0.040922	0.015166	0.038323	262.12	45.402
SQ00014812	C09	epothilone-B	microtubule stabilizing agent\|tubulin polymerization inhibitor	1.1111	26	20,362	4,441	0.29288	0.016025	0.012723	0.039328	0.014922	0.039402	252.2	41.456
SQ00014812	C10	epothilone-B	microtubule stabilizing agent\|tubulin polymerization inhibitor	0.3704	21	14,808	4,042	0.32061	0.017118	0.014178	0.038034	0.014602	0.039658	236.66	37.745
SQ00014812	C11	epothilone-B	microtubule stabilizing agent\|tubulin polymerization inhibitor	0.1235	25	14,874	4,130	0.31328	0.017762	0.013218	0.039233	0.014715	0.041283	236.07	40.428
SQ00014812	C12	epothilone-B	microtubule stabilizing agent\|tubulin polymerization inhibitor	0.0412	25	15,667	4,299	0.30954	0.017462	0.013678	0.037355	0.013536	0.041267	240.25	40.772
SQ00014812	C13	SB-743921	kinesin-like spindle protein inhibitor	10	16	15,526	3,629	0.31165	0.019028	0.020529	0.054577	0.016834	0.047151	232.77	28.17
SQ00014812	C14	SB-743921	kinesin-like spindle protein inhibitor	3.3333	24	20,484	4,205.5	0.23643	0.015012	0.012371	0.035361	0.012287	0.034829	237.12	40.893
SQ00014812	C15	SB-743921	kinesin-like spindle protein inhibitor	1.1111	26	22,998	4,499	0.22579	0.015112	0.011011	0.03405	0.011971	0.034556	245.57	43.964
SQ00014812	C16	SB-743921	kinesin-like spindle protein inhibitor	0.3704	25	22,845	4,393	0.22657	0.015261	0.011376	0.033367	0.011895	0.033984	247.62	44.407
SQ00014812	C17	SB-743921	kinesin-like spindle protein inhibitor	0.1235	25	21,358	4,246	0.22309	0.015207	0.011735	0.034534	0.011809	0.034925	236.3	42.564
SQ00014812	C18	SB-743921	kinesin-like spindle protein inhibitor	0.0412	26	23,216	4,372.5	0.22251	0.015127	0.011224	0.034305	0.011773	0.034121	245.16	44.673
SQ00014812	C19	bortezomib	NFkB pathway inhibitor\|proteasome inhibitor	20	7	8,169.5	3,438.5	0.35248	0.026761	0.037922	0.036935	0.012491	0.041821	172.33	22.137
SQ00014812	C20	bortezomib	NFkB pathway inhibitor\|proteasome inhibitor	20	7	7,603	3,118.5	0.37245	0.025683	0.038707	0.035654	0.013088	0.041966	173.61	21.829
SQ00014812	C21	bortezomib	NFkB pathway inhibitor\|proteasome inhibitor	20	8	7,470	2,981	0.33206	0.026256	0.037057	0.033422	0.012487	0.040402	168.79	21.059
SQ00014812	C22	bortezomib	NFkB pathway inhibitor\|proteasome inhibitor	20	7	7,544	3,102.5	0.34563	0.025415	0.041259	0.035316	0.01214	0.041502	170.33	21.274
SQ00014812	C23	bortezomib	NFkB pathway inhibitor\|proteasome inhibitor	20	9	7,318	3,093	0.33676	0.024264	0.036189	0.034117	0.012173	0.041199	159.18	21.352
SQ00014812	C24	bortezomib	NFkB pathway inhibitor\|proteasome inhibitor	20	7	8,142	3,031.5	0.36594	0.022918	0.040002	0.035212	0.012444	0.044201	165.41	19.742
SQ00014812	D01	terbinafine	fungal squalene epoxidase inhibitor	10	127	11,378	2,767	0.33394	0.017661	0.011217	0.041136	0.016075	0.036943	131.11	52.288
SQ00014812	D02	terbinafine	fungal squalene epoxidase inhibitor	3.3333	138	10,536	2,613	0.33893	0.018518	0.010508	0.042963	0.016719	0.037636	131.07	52.375
SQ00014812	D03	terbinafine	fungal squalene epoxidase inhibitor	1.1111	138	10,372	2,586.5	0.34573	0.019166	0.010908	0.043352	0.016823	0.036899	134.48	51.775
SQ00014812	D04	terbinafine	fungal squalene epoxidase inhibitor	0.3704	177	8,782.5	2,553.5	0.35731	0.022004	0.011695	0.047817	0.019113	0.040754	135.88	51.36
SQ00014812	D05	terbinafine	fungal squalene epoxidase inhibitor	0.1235	149	9,975	2,644	0.35225	0.020142	0.011666	0.045058	0.017219	0.038453	136.41	51.17
SQ00014812	D06	terbinafine	fungal squalene epoxidase inhibitor	0.0412	172	9,090	2,519	0.35468	0.020581	0.011382	0.046205	0.018128	0.039721	129.78	52.284
SQ00014812	D07	etizolam	benzodiazepine receptor agonist	10	167.5	9,194	2,588.5	0.35421	0.020408	0.011773	0.044836	0.017437	0.037489	128.54	51.147
SQ00014812	D08	etizolam	benzodiazepine receptor agonist	3.3333	162	9,562.5	2,532.5	0.35326	0.019685	0.010963	0.043342	0.016951	0.038679	127.36	51.957
SQ00014812	D09	etizolam	benzodiazepine receptor agonist	1.1111	138	10,328	2,699	0.3488	0.019079	0.011266	0.044025	0.016638	0.037636	129.19	51.572
SQ00014812	D10	etizolam	benzodiazepine receptor agonist	0.3704	159	9,832	2,527.5	0.34724	0.019015	0.01149	0.044256	0.016768	0.037905	121.62	50.64
SQ00014812	D11	etizolam	benzodiazepine receptor agonist	0.1235	170	9,123	2,503	0.3472	0.019614	0.01054	0.047169	0.017493	0.039364	117.89	50.558
SQ00014812	D12	etizolam	benzodiazepine receptor agonist	0.0412	157	9,396.5	2,468	0.35002	0.019245	0.010759	0.045662	0.017381	0.040249	119.17	52.205
SQ00014812	D13	12-O-tetradecanoylphorbol-13-acetate	PKC activator	8.106	40	8,648.5	2,452	0.37594	0.020075	0.021252	0.067548	0.019667	0.044871	121.8	28.521
SQ00014812	D14	12-O-tetradecanoylphorbol-13-acetate	PKC activator	2.702	91	10,206	2,439	0.37712	0.018708	0.013593	0.053984	0.017547	0.043394	120.48	38.9
SQ00014812	D15	12-O-tetradecanoylphorbol-13-acetate	PKC activator	0.9007	86	9,715	2,494.5	0.37814	0.01954	0.013536	0.054956	0.018224	0.044283	126.72	38.229
SQ00014812	D16	12-O-tetradecanoylphorbol-13-acetate	PKC activator	0.3002	65	10,045	2,671.5	0.37467	0.020537	0.015411	0.057021	0.018659	0.04788	138.27	37.238
SQ00014812	D17	12-O-tetradecanoylphorbol-13-acetate	PKC activator	0.1001	57	9,559	3,000	0.37963	0.020323	0.016284	0.062288	0.020801	0.051982	135.48	37.757
SQ00014812	D18	12-O-tetradecanoylphorbol-13-acetate	PKC activator	0.0334	53	9,959	2,958	0.36361	0.019795	0.016555	0.060624	0.019848	0.051196	134.55	35.958
SQ00014812	D19	lidamidine	adrenergic receptor agonist	10	156	9,807	2,545	0.34439	0.01895	0.009905	0.04063	0.014788	0.035841	120.8	52.978
SQ00014812	D20	lidamidine	adrenergic receptor agonist	3.3333	156	9,678.5	2,548	0.34477	0.019634	0.01008	0.040776	0.015688	0.037504	127.47	51.369
SQ00014812	D21	lidamidine	adrenergic receptor agonist	1.1111	158	9,745	2,522	0.33846	0.019681	0.00963	0.038641	0.014658	0.034965	129.51	53.283
SQ00014812	D22	lidamidine	adrenergic receptor agonist	0.3704	146	10,147	2,583	0.34462	0.018577	0.009649	0.038441	0.013994	0.034855	126.52	54.827
SQ00014812	D23	lidamidine	adrenergic receptor agonist	0.1235	123	11,191	2,648	0.32239	0.017364	0.009898	0.036078	0.013169	0.034564	127.22	50.938
SQ00014812	D24	lidamidine	adrenergic receptor agonist	0.0412	146	9,944	2,565.5	0.33217	0.018711	0.00889	0.039838	0.014274	0.03562	124.92	51.719
SQ00014812	E01	PF-03814735	Aurora kinase inhibitor	10	15	20,569	3,644	0.24411	0.01346	0.015026	0.037992	0.012886	0.033783	158.43	37.553
SQ00014812	E02	PF-03814735	Aurora kinase inhibitor	3.3333	24	22,343	4,313	0.24999	0.013578	0.013727	0.042248	0.013704	0.036069	213.39	44.71
SQ00014812	E03	PF-03814735	Aurora kinase inhibitor	1.1111	36	31,800	4,913	0.20318	0.012682	0.01097	0.040114	0.013834	0.03339	248.4	48.879
SQ00014812	E04	PF-03814735	Aurora kinase inhibitor	0.3704	37	32,759	4,954	0.19801	0.012727	0.011038	0.042029	0.015725	0.035243	246.55	49.368

End of preview. Expand in Data Studio

spaCR — Dose-Response example (LINCS Cell Painting)

Well-level Cell Painting profiles of one LINCS plate map, four replicate plates, cut to plate, well, compound, dose and eleven CellProfiler features, with two regression runs and two training runs made from them. It is the data behind Load test data… on spaCR's Dose-Response, Prediction Profiler, Run Compare, Run History and Training Runs screens (alpha features).

1,536 wells: 56 compounds at six doses (55 from 0.041 to 10 µM, one from 0.033 to 8.1 µM), MG-132 and bortezomib at one dose (20 µM) as positive controls, and DMSO vehicle wells (dose 0). spacr-example-dose.tar (one uncompressed tar, what spaCR downloads) holds everything; dose_plate.csv is also published loose.

Source

Cell Painting Gallery cpg0004-lincs, batch 2016_04_01_a549_48hr_batch1, file broad/workspace/profiles/2016_04_01_a549_48hr_batch1/<plate>/<plate>_augmented.csv.gz (median-aggregated, well-level CellProfiler profiles).
Plates SQ00014812, SQ00014813, SQ00014814, SQ00014815: four replicates of plate map C-7161-01-LM6-022. A549 cells, 48 h.

Files

dose_plate.csv: plate, well, compound, moa, dose_uM, then Cells_Number_Object_Number, Cells_AreaShape_Area, Nuclei_AreaShape_Area, Cells_AreaShape_FormFactor, Cells_Intensity_MeanIntensity_DNA, Cells_Intensity_MeanIntensity_Mito, Cells_Intensity_MeanIntensity_ER, Cells_Intensity_MeanIntensity_RNA, Cells_Intensity_MeanIntensity_AGP, Nuclei_Intensity_IntegratedIntensity_DNA, Cytoplasm_Granularity_1_Mito. Cells_Number_Object_Number is CellProfiler's median object number per well, which rises with the number of cells in a field; it is the response the Dose-Response button fits.
runs/<run>/results.csv and settings.json: ordinary least squares of that response on each compound's scaled log10 dose (0 = vehicle or another compound, 0.1–1 = 0.041–10 µM), raw (regression_raw) and divided by each plate's DMSO median (regression_dmso_normalised). Derived here, not part of the source.
training/: logistic regression (SGD) telling DMSO from ≥3.3 µM wells, trained on SQ00014812–14 and validated on SQ00014815, 20 epochs at learning rate 0.01 and 40 epochs at 0.001, in spaCR's training layout. Derived here.

Licence and citation

CC0 1.0, as the Cell Painting Gallery publishes it. Please cite:

Way GP, Natoli T, Adeboye A, et al. Morphology and gene expression profiling provide complementary information for mapping cell state. Cell Systems 13(11), 911–923 (2022). doi:10.1016/j.cels.2022.10.001
Weisbart E, Kumar A, Arevalo J, et al. Cell Painting Gallery: an open resource for image-based profiling. Nature Methods 21, 1775–1777 (2024). doi:10.1038/s41592-024-02399-z

Built by tools/build_dose_example_dataset.py in spaCR.

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