Journal: bioRxiv

Article Title: Using Imaris to rigorously track PET-defined sites of lung inflammation in Mycobacterium tuberculosis -exposed non-human primates

doi: 10.1101/2025.07.04.663191

Figure Lengend Snippet: Lesions identified for animal 40884 using Invicro VivoQuant ( Ai and B ) or Imaris ( Aii and C ) at different time points and different views. A : 3D view of lesions at 18 weeks post-infection in Invicro VivoQuant (i) and the same lesions in Imaris (ii) . B-C : Slice views of lesions identified with Invicro VivoQuant ( B ) or Imaris ( C ) at 6 (i, iv) , 14 (ii, v) , and 18 (iii, vi) weeks post-infection in both sagittal (i-iii) and coronal (iv-vi) slice views (see also and ). PET signal associated with the heart (shown by an arrow in Ai-ii ) was excluded from our analyses.

Article Snippet: We demonstrated that we can effectively track the same lesions identifiable in Invicro VivoQuant with Imaris ( and and ).

Techniques: Infection

Journal: bioRxiv

Article Title: Using Imaris to rigorously track PET-defined sites of lung inflammation in Mycobacterium tuberculosis -exposed non-human primates

doi: 10.1101/2025.07.04.663191

Figure Lengend Snippet: We illustrate how PET/CT scans are typically analyzed with Invicro VivoQuant, the standard proprietary packages for PET/CT data analysis ( A ), and with Imaris, proprietary packages typically used for fluorescent microscopy data analysis ( B ). A : With Invicro VivoQuant (i-iv) , the operator analyzes reconstructed 3D images by using 2D slices and manually labeling contours of the lesions, defined by PET signal. Invicro VivoQuant then provides various SUV characteristics, such as max SUV, for ether individual lesions or the whole lung. B : With Imaris (i-vi) , PET/CT DICOM files are imported as 2-channel images, and scans done at different times can be incorporated into the same Imaris file by adding new time frames. Then scans for different time points are aligned using “Correct for drift” routine by using landmarks (6 locations of spine vertebra). Then region of interest ( ROI ) is then identified around each suspected lesion and the data in ROI is processed using 3D routine “Surfaces”. All lesions then can be grouped into the specific group depending on the location of the lesion (e.g., lung vs. lymph nodes).

Article Snippet: We demonstrated that we can effectively track the same lesions identifiable in Invicro VivoQuant with Imaris ( and and ).

Techniques: Positron Emission Tomography-Computed Tomography, Microscopy, Labeling

Journal: bioRxiv

Article Title: Using Imaris to rigorously track PET-defined sites of lung inflammation in Mycobacterium tuberculosis -exposed non-human primates

doi: 10.1101/2025.07.04.663191

Figure Lengend Snippet: We show lesions identified for all animals using Invicro VivoQuant at different times post-infection from the right side 3D view for animals 44883 ( A ) and 44104 ( B ) at at 11 (i) , 16 (ii) and 22 (iii) weeks post-infection; and for animals 41634 ( C ) and 40884 ( D ) at 6 (i) , 14 (ii) and 18 (iii) weeks post-infection. PET signal associated with the heart (shown by an arrow in Ai ) was excluded from our analyses.

Article Snippet: We demonstrated that we can effectively track the same lesions identifiable in Invicro VivoQuant with Imaris ( and and ).

Techniques: Infection

Journal: bioRxiv

Article Title: Using Imaris to rigorously track PET-defined sites of lung inflammation in Mycobacterium tuberculosis -exposed non-human primates

doi: 10.1101/2025.07.04.663191

Figure Lengend Snippet: We analyzed PET/CT data from four Mtb-infected RMs (each with three PET/CT scans) either with Invicro VivoQuant, a standard software for PET/CT data analysis, or Imaris (Bitplane), software typically used for analysis of fluorescent microscopy data. For each lesion we plot maximum SUV as provided by Invicro VivoQuant (x axes) or maximum intensity as provided by Imaris (y axes), normalized using weight of the animal and 18F-FDG injection dose and multiplied by f = 10 (see ). We show data for animal 41883 ( A ), 44104 ( B ), 41634 ( C ), and 40884 ( D ) with n indicating the number of lesions detected in all scans and m being a regression slope between SUV values of Invicro VivoQuant vs. Imaris for all lesions or lesions found in individual scans; we show the regression lines in individual panels for all lesions. Scans done at different times are shown by different color intensity. The dashed line shows the slope of 1.

Article Snippet: We demonstrated that we can effectively track the same lesions identifiable in Invicro VivoQuant with Imaris ( and and ).

Techniques: Positron Emission Tomography-Computed Tomography, Infection, Software, Microscopy, Injection