Fig 2: The sizes of three-dimensional structures measured with CellSens software (Olympus); area of representative aggregates/colonies/spheres in specific cell line/media was marked and calculated accordingly to magnification of the microscope

Fig 3: Early CLT treatment shows dose-dependent efficacy in the reversible model. a Effects of MPA (30 mg kg−1) and CLT (LD-CLT, 1 mg kg−1; MD-CLT, 2 mg kg−1; HD-CLT, 3 mg kg−1) on 24-h urinary protein excretion in anti-Thy1.1 nephritic rats on day 5 after disease induction. b Glomerular histology revealed by PAS staining of kidney tissue sections from anti-Thy1.1 nephritic rats on day 5 after early treatment with MPA or different doses of CLT. Scale bars, 20 μm. c Effects of MPA and different doses of CLT on total glomerular cellularity on day 5 after disease induction. For each animal group, 150 glomeruli were selected and total glomerular cells were counted using cellSens Standard digital imaging software (Olympus). d Effects of MPA and different doses of CLT on ECM accumulation on day 5 after disease induction. For each animal group, 150 glomeruli were analyzed and ECM deposition was graded semiquantitatively as described in Methods. In panels a, c, and d data are mean ± s.d. (n = 5), results are representative of two independent experiments. *P < 0.05 vs. PBS group; # P < 0.05 vs. MPA group. Statistical significance was determined by one-way ANOVA with Tukey post hoc test. e Flow diagram of the early treatment of CLT or MPA against the reversible anti-Thy1.1 nephritis. Black triangle denotes intravenous treatment of CLT or MPA; black star denotes time points of nephrectomy while respective animals were sacrificed. A detailed description is given in Methods

Fig 4: Spatial patterns of IBI captured by PPM. (a) Extracted PPM signals of intranuclear inclusions overlaid with Hoechst-stained fluorescence image for nuclei visualization; (b) endometrioid carcinoma tissue section by PPM after deparaffinization showing a cluster of IBI; (c) IBI and basement membrane collagen PPM signals in kidney tissue section stained with hematoxylin for nuclei visualization and imaged using PPM; (d) Crystalloid structure of the IBI—nuclear inclusions captured in FFPE unstained tissue sections imaged by PPM with digital background correction; (e) gallery of nuclei segmented from Hoechst-stained renal cell carcinoma tissue imaged by fluorescence and overlaid with IBI acquired by PPM. All images acquired with Olympus BX63 microscope equipped with an Olympus DP80 camera using the CellSens acquisition software. Objectives: (b,c) Olympus UPlanApo 100x, (a,d) additional ×2 magnification lens used, (e) Olympus LUCPlanFLN 20x, with Olympus U_FUNA DAPI fluorescence filter cube. Original images acquired at a resolution of 1360 × 1024 px, resized and put into multi-panel figure using the GIMP image editor.

Fig 5: Micrographs illustrating dispersions of SC401 (left) and SC411 (right) at a 1:20 dilution in purified water. Taken with a BX43 Olympus Light Microscope using cellSens software for image capture and particle size measurement (1000X magnification).