confocal image displayed on maximum intensity projection zeiss lsm880  (Carl Zeiss)

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 therefore investigated if simply using actual maximum PET channel intensity, provided by Imaris for individual lesions, may nevertheless provide important information.

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 therefore investigated if simply using actual maximum PET channel intensity, provided by Imaris for individual lesions, may nevertheless provide important information.

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 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 therefore investigated if simply using actual maximum PET channel intensity, provided by Imaris for individual lesions, may nevertheless provide important information.

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

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: By using XYZ coordinates, provided by Imaris we plotted individual lesions detected in animals 41883 ( A ), 44104 ( B ), 41634 ( C ), and 40884 ( D ) at different time points after infection (times are denoted on individual panels). Note that the plots are from rear view of the animals (see also ). We also s how the total number of lesions detected at each time point as n . Lesions are plotted as spheres with the radius R = V/ (4 π ) where V is the PET volume determined by Imaris . Intensity of the color denotes scaled maximum PET signal intensity normalized to I max values for the largest maximum intensity for all lesions in all scans of a given animal; this also takes into account the actual injected FDG dose and weight of the animal . Black colors indicate animals that were asymptomatic and red colors indicate that the animal was diagnosed with active disease (TB).

Article Snippet: We therefore investigated if simply using actual maximum PET channel intensity, provided by Imaris for individual lesions, may nevertheless provide important information.

Techniques: Infection, Injection

Journal: Journal of Applied Clinical Medical Physics

Article Title: Evaluating artifact‐free four‐dimensional computer tomography with 16 cm detector array

doi: 10.1002/acm2.70056

Figure Lengend Snippet: Patient II: Images acquired for another patient case with his/her respiratory trace for the spherical and tumor targets. (A) The trace used for image acquisition of GT, 4D 16 , and 4D 4 . (B) MipCT and AveCT of the three with the traces of (A). iGTV in 4D 4 of tumor target II was 0.7 cm shorter than that of GT in the direction of motion. The patient is #8 in Table .

Article Snippet: The GT scan, gathered from all phases, were processed to generate the maximum‐intensity CT (MipCT) and the average‐intensity CT (AveCT) in Velocity (Varian Medical Systems, Palo Alto, CA).

Techniques:

Journal: Journal of Applied Clinical Medical Physics

Article Title: Evaluating artifact‐free four‐dimensional computer tomography with 16 cm detector array

doi: 10.1002/acm2.70056

Figure Lengend Snippet: Patient III: Images acquired for another patient case with his/her respiratory trace and tumor target. (A) The trace used for image acquisition of GT, 4D 16 , and 4D 4 . (B) MipCT and AveCT of the three with the traces of (A). iGTV of 4D 4 of tumor target III was 0.5 cm shorter than that of GT in the direction of motion. The patient is #9 in Table .

Article Snippet: The GT scan, gathered from all phases, were processed to generate the maximum‐intensity CT (MipCT) and the average‐intensity CT (AveCT) in Velocity (Varian Medical Systems, Palo Alto, CA).

Techniques:

Journal: Journal of Applied Clinical Medical Physics

Article Title: Evaluating artifact‐free four‐dimensional computer tomography with 16 cm detector array

doi: 10.1002/acm2.70056

Figure Lengend Snippet: Overlap ratios of targets in phase images, MipCT, and MipCT with margins of 4D 16 and 4D 4 and the ratio averaged across all phases (Ave) to target in each comparable GT image. 16 cm_I and 4 cm_I stand for 4D 16 and 4D 4 , respectively, of patient I. For each image, three sets of the ratio are presented for three patients, respectively, from left to right; each set included the ratios for 4D 16 and 4D 4 .

Article Snippet: The GT scan, gathered from all phases, were processed to generate the maximum‐intensity CT (MipCT) and the average‐intensity CT (AveCT) in Velocity (Varian Medical Systems, Palo Alto, CA).

Techniques: