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30 results for “3D histology”
Robust joint registration of multiple stains and MRI for multimodal 3D histology reconstruction: Application to the Allen human brain atlas
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A high-throughput 3D X-ray histology facility for biomedical research and preclinical applications - Supplementary Data
<p><strong>Videos</strong></p><ul><li><strong>Video 1</strong> A video going through the Z stack in single slices. This is a cross- sectional view of the XRH image stack along the XY plane. XRH datasets are normally oriented (resliced) in a way that a scroll through the stack along the XY plane emulates the physical histology slicing of the tissue.</li><li><strong>Video 2 </strong>A video going through the Y stack in single slices. This is a cross- sectional view of the XRH image stack along the XZ plane. XRH datasets are normally oriented (resliced) in a way that a scroll through the stack along the XY plane emulates the physical histology slicing of the tissue.</li><li><strong>Video 3 </strong>A video going through the X stack in single slices. This is a cross- sectional view of the XRH image stack along the YZ plane. XRH datasets are normally oriented (resliced) in a way that a scroll through the stack along the XY plane emulates the physical histology slicing of the tissue.</li><li><strong>Video 4 </strong>3D X-ray histology (XRH) is a µCT -based workflow tailored to fit seamlessly into current histology workflows in biomedical and pre-clinical research, as well as clinical histopathology. Microanatomical detail can be captured from standard (non-stained) formalin-fixed and paraffin-embedded (FFPE) tissue blocks.</li><li><strong>Video 5</strong> Average Intensity Projection (AIP) of the sample through the Histologically relevant plane. This is a 2D visualisation rendering the Average Intensity of 20x single XY slices along the z-axis of the stack. XRH datasets are normally oriented (resliced) in a way that a scroll through the stack along the XY plane emulates the physical histology slicing of the tissue.</li><li><strong>Video 6 </strong>Maximum Intensity Projection (MIP) of the sample through the Histologically relevant plane. This is a 2D visualisation rendering the Maximum Intensity of 20x single XY slices along the z-axis of the stack. XRH datasets are normally oriented (resliced) in a way that a scroll through the stack along the XY plane emulates the physical histology slicing of the tissue.</li><li><strong>Video 7 </strong>Standard deviation projection of the sample going through the histologically relevant plane. This is a 2D visualisation rendering the Standard Deviation of 20x single XY slices along the z- axis of the stack. XRH datasets are normally oriented (resliced) in a way that a scroll through the stack along the XY plane emulates the physical histology slicing of the tissue.</li></ul><p><i>* <strong>Videos 5 -7</strong> are also referred to as "thick-slice rolls" </i>- <i>Thick-slice rolling is a 2D thick-slice viewing that allows rolling of a pre-selected number of slices (n) along the z-axis of the 3D data. A single thick-slice roll forwards is accomplished by translating the thick-slice by one single slice forwards; that is moving forward by one (+1) slice from the first and nth element and reapplying the criteria or operations to the new slice sub-stack.</i><br> </p><p><strong>The questionnaire used to collect feedback about the needs of the XRH community.</strong></p><ul><li>Survey.docx</li><li>Survey.pdf</li></ul><p><br><strong>Exemplar report of a semi-automatically generated augmented PDF file</strong> that contain sample information, imaging settings, still images with descriptive figure legends, and links to corresponding online videos</p><ul><li>DEMO02019-FFPE_report_99EbPXG.pdf</li></ul><p> </p><p>= = = = = = = = = = = = = = = = <br><strong>System performance data ZIP</strong><br>= = = = = = = = = = = = = = = = </p><p>This ZIP file contains imaging data collected through different systems and setups at the XRH facility at the μ-VIS X-ray Imaging Centre at the University of Southampton for the purpose of acceptance and/or system performance characterisation. Below is an overview of the folder structure and its contents</p><p>The following files are X-ray imaging data collected on September 28, 2017, using the Med-X system and a Jima phantom at 55 kV peak and 7 Watts. </p><ul><li>20170928_MEDX_1642_JIMA_55kVp7W-2.tif</li><li>20170928_MEDX_1642_JIMA_55kVp7W.tif</li><li>20170928_MEDX_1642_JIMA_55kVp7W.tif.profile.xml</li></ul><p>This PDF document is related to a QRM MicroCT bar pattern phantom, and its specifications</p><ul><li>QRM-MicroCT-Barpattern-Phantom.pdf</li></ul><p>Graphs showing the calculated focal-spot size as a function of the X-ray power (W) for the Molybdenum rotating target calculated using Edge Modulation function testing. The performance is then compared with the performance of the Reflection target across the same range of powers. Raw data can be found in XRH_QRM_Refl-vs-Rot-TargetComparison_SingleReconSlices_5umPixelSize folder. Test performed in July 2021. </p><ul><li>XRH_202107_MoRot-testing_EdgeModFunction-QRMrecons+RotReflCompar.png</li></ul><p> </p><p><i><strong>/ XRH-XT-H-225-ST_FocalSpots</strong></i><br>This directory contains radiographic data collected using the XRH system with a JIMA phantom and MoRt (Molybdenum rotating), TT (Transmission), and Reflection targets.</p><ul><li>20200113_XRH_Jima test MoRT 55kV 15W.tif, 20200113_XRH_Jima test MoRT 55kV 30W.tif, etc.: <br>These files represent radiographs taken on January 13, 2020, using the XRH system, Jima phantom, MoRT target at 55 kVp and varying wattages.</li><li>20200207_XRH_JIMA 80kV TT1a.tif, 20200207_XRH_JIMA 80kV TT1b.tif, etc.<br>Similar to the above, these files are from February 7, 2020, and use 80 kVp with a TT target.</li><li>20231115_XRH_reflW_80kVp6W.tif, 20231115_XRH_reflW_80kVp6W_02.tif, etc.<br>These files are from November 15, 2023, and collected using the XRH system with a Reflection target at 80 kVp and 6 Watts.</li></ul><p><i><strong>/ XRH_QRM_Refl-vs-Rot-TargetComparison_SingleRadioFromCTs_5umPixelSize</strong></i><br>This directory contains single radiographs taken with a pixel size of 5 micrometers using the Molybdenum rotating (MoRt), and the Reflection target using tungsten (W) and Molybdenum (Mo) metals.</p><p><i><strong>/ XRH_QRM_Refl-vs-Rot-TargetComparison_SingleReconSlices_5umPixelSize</strong></i><br>This directory contains sinlge reconstruction slices of the setups mentioned above. Slices are exported from CT volumes and were used for the Edge Modulation function study. </p><p>For interpretation of the filenames in the folders listed above please see below and refer to specific files and folders for detailed information and results related to each imaging session:</p><ul><li><i><xx>kVp or <xx>kV </i>:Imaging at a peak voltage of <xx> kVp.</li><li><i><y>W</i> :Imaging at <y> Watts;<i> </i>"." is represented with "-"; i.e. 20210705_XRH_2766_PJB_TEST03552-EQPMT_W_6-9W is acquired using a power of 6.9 W</li><li><i>MoRt, TT, Refl </i> :Molybdenum, Transmission, and Reflection targets, respectively.</li><li><i>_W_ and _Mo_ </i> :Tungsten and Molybdenum target materials.</li><li><i>_horiz</i> :Reconstruction slices in line with the X-ray beam's propagation direction.</li><li><i>_vert</i> :Reconstruction slices normal to the X-ray beam's propagation direction and parallel to the detector plane.</li></ul>
A high-throughput 3D X-ray histology facility for biomedical research and preclinical applications - Underlying Data
<p><strong>Video files and logs</strong></p> <p>Single-slice and thick-slice roll* source videos are included. Each video is accompanied by a .txt log that contains information about the source file, slice thickness, and a brief description of the visualization mode.</p> <p>List of files:</p> <ul> <li>20211019-23h59m_20xAvgInt.mp4</li> <li>20211019-23h59m_20xAvgInt.txt</li> <li>20211019-23h59m_20xMaxInt.mp4</li> <li>20211019-23h59m_20xMaxInt.txt</li> <li>20211019-23h59m_20xStDev.mp4</li> <li>20211019-23h59m_20xStDev.txt</li> <li>20211019-23h59m_XYSliceRoll.mp4</li> <li>20211019-23h59m_XYSliceRoll.txt</li> <li>20211019-23h59m_XZSliceRoll.mp4</li> <li>20211019-23h59m_XZSliceRoll.txt</li> <li>20211019-23h59m_YZSliceRoll.mp4</li> <li>20211019-23h59m_YZSliceRoll.txt</li> </ul> <p>* <em>Thick-slice rolling is a 2D thick-slice viewing that allows rolling of a pre-selected number of slices (n) along the z-axis of the 3D data. A single thick-slice roll forwards is accomplished by translating the thick-slice by one single slice forwards; that is moving forward by one (+1) slice from the first and nth element and reapplying the criteria or operations to the new slice sub-stack.</em></p> <p><strong>Volume XRH data</strong><br> These are processed raw volume file saved in .raw and/or .tiff format, which are resliced to a histology-relevant orientation and/or have been enhanced using noise reduction (3D median filter) and/or ct-artefact removal techniques (e.g. cBC identifies a bandpass filter used to remove intensity variations originating from the histology cassette).</p> <p>List of volume files:</p> <ul> <li><strong>32220_20200703_XRH_2504_OLK_DEMO02019-FFPE_1620x1959x164x16bit.raw</strong> <ul> <li>sample: Human lung adenocarcinoma</li> <li>histology-relevant resliced volume (2x2x2 3D medial filter applied)</li> <li>import as 1620 x 1959 x 164 x 16-bit, big-endian; voxel edge size (mm): 0.0160042 isotropic</li> </ul> </li> <li><strong>cBC_32220_20200703_XRH_2504_OLK_DEMO02019-FFPE_1588x1674x164x16bit.raw</strong> <ul> <li>sample: Human lung adenocarcinoma</li> <li>cassette artefacts background correction (bandpass) of volume 32220_20200703_XRH_2504_OLK_DEMO02019-FFPE_1620x1959x164x16bit.raw</li> <li>import as 1620 x 1959 x 164 x 16-bit, big-endian; voxel edge size (mm): 0.0160042 isotropic</li> </ul> </li> <li><strong>Med3D_HPass_2111_20190606_MEDX_2234_EH_HN2_recon_2000x1952x501x32bit.raw</strong> <ul> <li>sample: Human head and neck tumour</li> <li>histology-relevant resliced volume (1x1x1 3D medial filter applied)</li> <li>import as 2000 x 1952 x 501 x 32-bit, big-endian; voxel edge size (mm): 0.00999782 isotropic</li> </ul> </li> </ul> <p><strong>Conventional Histology and correlative imaging</strong></p> <ul> <li><strong>HN2_Level001_MEDX080_Manual_BW_Series4.tif</strong> <ul> <li>H&E histology slice of the human head and neck tumour sample shown in "Med3D_HPass_2111_20190606_MEDX_2234_EH_HN2_recon_2000x1952x501x32bit.raw"</li> </ul> </li> <li><strong>HN2_Level001_MEDX080_Manual_BW</strong> <ul> <li>manual landmark selection used for registering the conventional histology slice onto the μCT slice</li> </ul> </li> <li><strong>HN2_MEDX_rotated_0080.tif</strong> <ul> <li>Slice 80 from volume "Med3D_HPass_2111_20190606_MEDX_2234_EH_HN2_recon_2000x1952x501x32bit.raw" that corresponds to histological slice "HN2_Level001_MEDX080_Manual_BW"</li> </ul> </li> </ul>
3d Virtual Patho-Histology of Lung Tissue from Covid19 Patients based on Phase Contrast X-ray Tomography
<p>X-ray phase contrast tomographys datasets of lung tissue from 6 Covid-19 patients (paraffin embedded unstained tissue), and one control tissue (healthy lung, in fixative solution). The data has been recorded as part of the Covid-19 Call for Proposals at DESY April 2020 at the GINIX instrument, beamline P10 of the PETRAIII storage ring at 8keV. Three different datasets are included in a single tar archive for each sample: (i) overview scan (up to 4mm cross section ) from stitching different tomograms, (ii) 1mm cylindrical punch, and (iii) cone-beam zoom tomogram recorded with waveguide illumination. </p> <p>voxel sizes: (i) 1.3µm, (ii) 650nm, (iii) 167nm. </p> <p>3 datasets per sample, raw format, voxel numbers given in Filename, single (32bit real)</p> <p> </p>
3d virtual histology of the human hippocampus based on phase-contrast computed-tomography
<p>This data package contains:<br> - exemplary data sets of multiscale imaging of the human hippocampus as raw-files (gray values, segmentation masks)<br> - object properties as xlsx-files (for all data sets)<br> - analysis scripts (based on matlab, R, python)</p>
FIGURE 8. 3D in Contribution to the morphological description of the marine leech, Ozobranchus margoi (Apáthy) (Rhynchobdellida: Ozobranchidae) by using combined histology, micro-CT and SEM
FIGURE 8. 3D volume renderings of O. margoi using the micro-CT technology. Contrast enhancement to expose the denser parts. A, dorsal view of the whole body until the posterior sucker (ps) enouncing the digestive system. From the posterior intestine (pi) two lateral post ceca are starting (pca). Four pairs of blind ending lateral diverticula (ld) are diverting from the posterior intestine that finally enlarge to form a sac-like structure. Arrows indicate the two lateral blind-ended sacks in the last sack of the posterior intestine. B, frontal view of the anterior sucker (as) showing the four lines of lateral columnar glands (gl) and a central gland-like structure separated from the other (arrow). Scale bar = 1mm.
Histology archive for 3D woolly mammoth study
<p> </p> <table> <tbody> <tr> <td> <p>Image #</p> </td> <td> <p>Block #</p> </td> <td> <p>Staining</p> </td> <td> <p>Notes</p> </td> <td> <p>Microscope</p> </td> </tr> <tr> <td> <p>1. </p> </td> <td> <p>3</p> </td> <td> <p>Van Gieson + Giemsa</p> </td> <td> <p>Remaining epidermis, derma and subcutaneous tissue, striated muscle</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>2. </p> </td> <td> <p>3</p> </td> <td> <p>Van Gieson + Giemsa</p> </td> <td> <p>Remaining epidermis, derma and subcutaneous tissue, striated muscle</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>3. </p> </td> <td> <p>3</p> </td> <td> <p>Van Gieson + Giemsa</p> </td> <td> <p>Remaining epidermis, derma and subcutaneous tissue, striated muscle</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>4. </p> </td> <td> <p>3</p> </td> <td> <p>Van Gieson + Giemsa</p> </td> <td> <p>Remaining epidermis, derma and subcutaneous tissue, striated muscle</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>5. </p> </td> <td> <p>3</p> </td> <td> <p>Van Gieson + Giemsa</p> </td> <td> <p>Remaining epidermis, derma and subcutaneous tissue, striated muscle</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>6. </p> </td> <td> <p>7</p> </td> <td> <p>Van Gieson + Giemsa</p> </td> <td> <p>Remaining epidermis, derma and subcutaneous tissue, striated muscle</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>7. </p> </td> <td> <p>7</p> </td> <td> <p>Van Gieson + Giemsa</p> </td> <td> <p>Remaining epidermis, derma and subcutaneous tissue, striated muscle</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>8. </p> </td> <td> <p>7</p> </td> <td> <p>Van Gieson + Giemsa</p> </td> <td> <p>Remaining epidermis, derma and subcutaneous tissue, striated muscle</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>9. </p> </td> <td> <p>10</p> </td> <td> <p>Eosin</p> </td> <td> <p>Derma and subcutaneous tissue (adipose?)</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>10. </p> </td> <td> <p>10</p> </td> <td> <p>Eosin</p> </td> <td> <p>Epidermis, derma and subcutaneous tissue (adipose?), contaminants</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>11. </p> </td> <td> <p>10</p> </td> <td> <p>Eosin</p> </td> <td> <p>Subcutaneous tissue (adipose?)</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>12. </p> </td> <td> <p>7</p> </td> <td> <p>Giemsa</p> </td> <td> <p>Hair follicle with hair attached</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>13. </p> </td> <td> <p>7</p> </td> <td> <p>Giemsa</p> </td> <td> <p>Hair follicle with hair attached</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>14. </p> </td> <td> <p>7</p> </td> <td> <p>Giemsa</p> </td> <td> <p>Hair follicle with hair attached</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>15. </p> </td> <td> <p>7</p> </td> <td> <p>Giemsa</p> </td> <td> <p>Hair follicle with hair attached</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>16. </p> </td> <td> <p>7</p> </td> <td> <p>Giemsa</p> </td> <td> <p>Hair follicle with hair attached</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>17. </p> </td> <td> <p>7</p> </td> <td> <p>Giemsa</p> </td> <td> <p>Hair follicle with hair attached</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>18. </p> </td> <td> <p>7</p> </td> <td> <p>Giemsa</p> </td> <td> <p>Hair follicle with hair attached</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>19. </p> </td> <td> <p>7</p> </td> <td> <p>Giemsa</p> </td> <td> <p>Hair follicle with hair attached</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>20. </p> </td> <td> <p>7</p> </td> <td> <p>Giemsa</p> </td> <td> <p>Hair follicle with hair attached</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>21. </p> </td> <td> <p>7</p> </td> <td> <p>Giemsa</p> </td> <td> <p>Hair follicle with hair attached</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>22. </p> </td> <td> <p>7</p> </td> <td> <p>Giemsa</p> </td> <td> <p>Hair follicle with hair attached</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>23. </p> </td> <td> <p>7</p> </td> <td> <p>Giemsa</p> </td> <td> <p>Hair follicle with hair attached</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>24. </p> </td> <td> <p>7</p> </td> <td> <p>Giemsa</p> </td> <td> <p>Hair follicle with hair attached</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>25. </p> </td> <td> <p>7</p> </td> <td> <p>Giemsa</p> </td> <td> <p>Hair follicle with hair attached</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>26. </p> </td> <td> <p>7</p> </td> <td> <p>Giemsa</p> </td> <td> <p>Hair follicle with hair attached</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>27. </p> </td> <td> <p>7</p> </td> <td> <p>Giemsa</p> </td> <td> <p>Hair follicle with hair attached</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>28. </p> </td> <td> <p>5</p> </td> <td> <p>Van Gieson + Giemsa</p> </td> <td> <p>Striated muscle</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>29. </p> </td> <td> <p>5</p> </td> <td> <p>Van Gieson + Giemsa</p> </td> <td> <p>Striated muscle</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>30. </p> </td> <td> <p>5</p> </td> <td> <p>Van Gieson + Giemsa</p> </td> <td> <p>Striated muscle</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>31. </p> </td> <td> <p>5</p> </td> <td> <p>Van Gieson + Giemsa</p> </td> <td> <p>Striated muscle</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>32. </p> </td> <td> <p>5</p> </td> <td> <p>Van Gieson + Giemsa</p> </td> <td> <p>Striated muscle</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>33. </p> </td> <td> <p>5</p> </td> <td> <p>Van Gieson + Giemsa</p> </td> <td> <p>Striated muscle</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>34. </p> </td> <td> <p>5</p> </td> <td> <p>Van Gieson + Giemsa</p> </td> <td> <p>Striated muscle</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>35. </p> </td> <td> <p>5</p> </td> <td> <p>Van Gieson + Giemsa</p> </td> <td> <p>Striated muscle</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>36. </p> </td> <td> <p>5</p> </td> <td> <p>Van Gieson + Giemsa</p> </td> <td> <p>Striated muscle</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>37. </p> </td> <td> <p>5</p> </td> <td> <p>Van Gieson + Giemsa</p> </td> <td> <p>Striated muscle</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>38. </p> </td> <td> <p>5</p> </td> <td> <p>Van Gieson + Giemsa</p> </td> <td> <p>Striated muscle</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>39. </p> </td> <td> <p>8</p> </td> <td> <p>DAPI</p> </td> <td> <p>Striated muscle</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>40. </p> </td> <td> <p>n/a</p> </td> <td> <p>DAPI</p> </td> <td> <p>Striated muscle</p> </td> <td> <p>Olympus FV3000</p> </td> </tr> <tr> <td> <p>41. </p> </td> <td> <p>3</p> </td> <td> <p>Van Gieson + Giemsa</p> </td> <td> <p>Other (sebaceous glands?)</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>42. </p> </td> <td> <p>3</p> <p> </p> </td> <td> <p>Van Gieson + Giemsa</p> </td> <td> <p>Other (sebaceous glands?)</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>43. </p> </td> <td> <p>10</p> </td> <td> <p>Van Gieson</p> </td> <td> <p>Other (myelinated nerve fibers?)</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>44. </p> </td> <td> <p>8</p> </td> <td> <p>DAPI</p> </td> <td> <p>Other (vessel?)</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>45. </p> </td> <td> <p>8</p> </td> <td> <p>DAPI</p> </td> <td> <p>Other (vessel?)</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>46. </p> </td> <td> <p>8</p> </td> <td> <p>DAPI</p> </td> <td> <p>Other (vessel?)</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>47. </p> </td> <td> <p>7</p> </td> <td> <p>DAPI</p> </td> <td> <p>Other (vessel?)</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>48. </p> </td> <td> <p>7</p> </td> <td> <p>DAPI</p> </td> <td> <p>Other (vessel?)</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>49. </p> </td> <td> <p>7</p> </td> <td> <p>Giemsa</p> </td> <td> <p>Bacterial contaminants (hair follicle lumen?)</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>50. </p> </td> <td> <p>7</p> </td> <td> <p>Giemsa</p> </td> <td> <p>Bacterial contaminants (hair follicle lumen?)</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>51. </p> </td> <td> <p>7</p> </td> <td> <p>Giemsa</p> </td> <td> <p>Bacterial contaminants</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>52. </p> </td> <td> <p>7</p> </td> <td> <p>Giemsa</p> </td> <td> <p>Bacterial contaminants</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>53. </p> </td> <td> <p>7</p> </td> <td> <p>Giemsa</p> </td> <td> <p>Bacterial contaminants</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>54. </p> </td> <td> <p>7</p> </td> <td> <p>Giemsa</p> </td> <td> <p>Bacterial contaminants (blood vessel?)</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>55. </p> </td> <td> <p>7</p> </td> <td> <p>Giemsa</p> </td> <td> <p>Bacterial contaminants in derma</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>56. </p> </td> <td> <p>9</p> </td> <td> <p>DAPI</p> </td> <td> <p>Contaminants in the remnants of muscle fascia</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>57. </p> </td> <td> <p>8</p> </td> <td> <p>Van Gieson + Eosin</p> </td> <td> <p>Septate fungal hyphae, muscle tissue</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>58. </p> </td> <td> <p>3</p> </td> <td> <p>Van Gieson + Giemsa</p> </td> <td> <p>Fungi</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>59. </p> </td> <td> <p>3</p> </td> <td> <p>Van Gieson + Giemsa</p> </td> <td> <p>Fungi</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>60. </p> </td> <td> <p>3</p> </td> <td> <p>Van Gieson + Giemsa</p> </td> <td> <p>Derma and subcutaneous tissue, contaminants</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>61. </p> </td> <td> <p>3</p> </td> <td> <p>Van Gieson + Giemsa</p> </td> <td> <p>Unidentified inclusions in derma (parasitic?)</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>62. </p> </td> <td> <p>7</p> </td> <td> <p>Van Gieson + Giemsa</p> </td> <td> <p>Unidentified inclusions in derma (parasitic?)</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>63. </p> </td> <td> <p>7</p> </td> <td> <p>DAPI</p> </td> <td> <p>Unidentified inclusions in derma, bacterial contaminants</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>64. </p> </td> <td> <p>7</p> </td> <td> <p>Van Gieson</p> </td> <td> <p>Contaminating organisms in derma (parasitic?)</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>65. </p> </td> <td> <p>10</p> </td> <td> <p>Van Gieson + Giemsa</p> </td> <td> <p>Contaminating organisms in derma, multiple</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>66. </p> </td> <td> <p>10</p> </td> <td> <p>Van Gieson</p> </td> <td> <p>Unidentified inclusions in derma (parasitic?), fungi</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> <tr> <td> <p>67. </p> </td> <td> <p>10</p> </td> <td> <p>Van Gieson</p> </td> <td> <p>Contaminating organisms in derma (parasitic?)</p> </td> <td> <p>Zeiss AXIO Scope.A1 microscope</p> </td> </tr> </tbody> </table>
Fig. 15 in Comparative 3D microanatomy and histology of the eyes and central nervous systems in coleoid cephalopod hatchlings
Fig. 15 Loligo vulgaris hatchling: histology of the head region (transversal sections; Richardson staining; see also interactive supplementary figure 5). a Overview with selected planes B-H (3D reconstruction; left side view). b Brachial crown with arms and tentacles. c Base of brachial crown near mouth opening. d Midline of eyes, radula. e Lobus opticus just behind the eyes, anterior basal lobe. f Central lobus opticus with optic commissure, pedal lobe. g Posterior lobus opticus, statocysts with statoliths. h Palliovisceral lobes just behind the lobus opticus, statocysts. Labels: a 1–4=arms 1–4, abl=anterior basal lobe, aco=anterior chamber organ, doc=dorsal optic commissure, es=esophagus, ey= eye, fu=funnel, ibl=inferior buccal lobe, le=lens, ipl=inner plexiform layer, mcl=magnocellular lobe, noai=inferior anterior oculomotoric nerve, of=olfactory organ, ofl=olfactory lobe, ol=optic lobe (medullar core), opl=outer plexiform layer, pdc=peduncle commissure, pdl= peduncle lobe, pl=pedal lobe, pvl=palliovisceral lobe, ra=radula, re=retina, sl=statolith, st=statocyst, svl=subvertical lobe, t=tentacle, tp=tentacular pocket, voc=ventral optic commissure, vtl=vertical lobe; arrowhead crossing of first-order giant axons
Fig. 14 in Comparative 3D microanatomy and histology of the eyes and central nervous systems in coleoid cephalopod hatchlings
Fig. 14 Idiosepius notoides hatchling: histology of the head region (transversal sections; Richardson staining; see also interactive supplementary figure 4). a Overview with selected planes B-H (3D reconstruction; left side view). b Brachial crown with arms and tentacles. c Base of brachial crown near mouth opening, buccal mass. d Midline of eyes, brachial lobe. e Lobus opticus just behind eyes. f Central lobus opticus with optic commissure, anterior funnel. g Posterior lobus opticus, statocysts with statoliths. h Palliovisceral lobes just behind the lobus opticus, statocysts. Labels: a 1–4=arms 1–4, bl=brachial lobe, bm=buccal mass, es= esophagus, ey=eye, fu=funnel, ifl=inferior frontal lobe, le=lens, mbl=median basal lobe, np=pallial nerve, oc=optic commissure, of=olfactory organ, ol=optic lobe (medullar core), opl=outer plexiform layer, pdl=peduncle lobe, pl=pedal lobe, pvl=palliovisceral lobe, ra=radula, rc=radula cartilage, re=retina, sfl=superior frontal lobe, sl= statolith, st=statocyst, t=tentacle, tp=tentacular pocket
Fig. 11 in Comparative 3D microanatomy and histology of the eyes and central nervous systems in coleoid cephalopod hatchlings
Fig. 11 Sepia officinalis hatchling: histology of the head region (transversal sections; Richardson staining; see also interactive supplementary figure 1). a Overview with selected planes B-H (3D reconstruction; left side view). b Brachial crown with arms and tentacles. c Base of brachial crown near mouth opening. d Midline of eyes, buccal mass, and anterior funnel. e Lobus opticus just behind the eyes. f Central lobus opticus with optic commissure. g Posterior lobus opticus, statocysts with statoliths. h Palliovisceral lobes just behind the lobus opticus. Labels: a 1–4= arms 1–4, abl=anterior basal lobe, aco=anterior chamber organ, asg=anterior salivary gland, bl=brachial lobe, bm=buccal mass, cc=cerebral connective, dg=digestive gland, es=esophagus, ey=eye, fu=funnel, le=lens, mbl=median basal lobe, mcl= magnocellular lobe, np=pallial nerve, oc=optic commissure, of= olfactory organ, ol=optic lobe (medullar core), opl=outer plexiform layer, pdc=peduncle commissure, pl=pedal lobe, psd= posterior salivary duct, psg=posterior salivary gland, pvl=palliovisceral lobe, ra=radula, rc=radula cartilage, re=retina, sl=statolith, st=statocyst, t=tentacle, tp=tentacular pocket, vtl=vertical lobe
Fig. 10 3D in Comparative 3D microanatomy and histology of the eyes and central nervous systems in coleoid cephalopod hatchlings
Fig. 10 3D reconstruction of the anterior subesophageal mass (comparative ventral views). a Sepia officinalis, b Rossia macrosoma, c Sepietta obscura, d Idiosepius notoides, e Loligo vulgaris, f Octopus vulgaris. abrl=anterior brachial lobe, bl=brachial lobe, bmc=brachiomagnocellular connective, bpc= brachio-pedal connective, bpvc= brachio-palliovisceral connective, nas=superior antorbital nerve, noa=anterior oculomotoric nerve, noai=inferior anterior oculomotoric nerve, nopa= anterior inferior ophthalmic nerve, pbrl=posterior brachial lobe, pl=pedal lobe
Fig. 8 Supraesophageal neuropils. 3D in Comparative 3D microanatomy and histology of the eyes and central nervous systems in coleoid cephalopod hatchlings
Fig. 8 Supraesophageal neuropils. 3D reconstruction of the central nervous system around the brachial lobe (comparative left lateral and frontal views; enlarge to 100 % in the PDF viewer; A-F different scales). a Sepia officinalis, b Rossia macrosoma, c Sepietta obscura, d Idiosepius notoides, e Loligo vulgaris, f Octopus vulgaris. Labels: 14=olfactory nerve, 23=sympathic nerve, abl=anterior basal lobe, bbrc=bucco-brachial connective, cbc=cerebro-buccal connective, cbrc=cerebro-brachial
Fig. 7 Subesophageal neuropils. 3D in Comparative 3D microanatomy and histology of the eyes and central nervous systems in coleoid cephalopod hatchlings
Fig. 7 Subesophageal neuropils. 3D reconstruction of the central nervous system: supraesophageal and subesophageal neuropils (comparative left lateral and frontal views; enlarge to 100 % in the PDF viewer; A-F different scales). a Sepia officinalis, b Rossia macrosoma, c Sepietta obscura, d Idiosepius notoides, e Loligo vulgaris, f Octopus vulgaris. Labels: 1=inferior antorbital nerve, 2=superior antorbital nerve, 3=collar nerve, 4=crista nerve, 5=anterior funnel nerve, 6=median funnel nerve, 7=posterior funnel nerve, 8=anterior oculomotoric nerve, 9=inferior anterior oculomotoric nerve, 10=superior anterior oculomotoric nerve, 11=posterior oculomotoric nerve, 12=inferior posterior oculomotoric
Fig. 13 in Comparative 3D microanatomy and histology of the eyes and central nervous systems in coleoid cephalopod hatchlings
Fig. 13 Sepietta obscura hatchling: histology of the head region (transversal sections; b,c,e,h: Azan staining; d,f,g: Trichrome de Masson staining; see also interactive supplementary figure 3). a Overview with selected planes BH (3D reconstruction; left side view). b Brachial crown with arms and tentacles. c Beak and base of brachial crown. d Midline of eyes, brachial lobe. e Central lobus opticus just behind the eyes, anterior funnel. f Lobus opticus with optic commissure. g Posterior lobus opticus, statocysts with statoliths. h Stellate ganglion, gills, digestive gland. Labels: a 1–4=arms 1–4, aco= anterior chamber organ, bk=beak, bl=brachial lobe, dbl= dorsal basal lobe, dg=digestive gland, es=esophagus, ey=eye, fu=funnel, g=gill, ifl=inferior frontal lobe, le=lens, mbl=medi- an basal lobe, np=pallial nerve, oc=optic commissure, of=olfactory organ, ol=optic lobe (medullar core), opl=outer plexiform layer, pdc=peduncle commissure, pdl=peduncle lobe, pl= pedal lobe, re=retina, sbl=superior buccal lobe, sfl=superior frontal lobe, sg=stellate ganglion, sl=statolith, st=statocyst, t=tentacle, tp=tentacular pocket, vtl=vertical lobe
Fig. 4 in Comparative 3D microanatomy and histology of the eyes and central nervous systems in coleoid cephalopod hatchlings
Fig. 4 Comparative retina histology (ventral portion; transversal sections at the level of lens centers). a Sepia officinalis (Richardson), b Rossia macrosoma (Trichrome de Masson), c Sepietta obscura (Trichrome de Masson), d Idiosepius notoides (Richardson), e Loligo vulgaris (Richardson), f Octopus vulgaris (Azan). Labels: bsm=basal membrane, ds=distal segments of photoreptors, ps=proximal segments of photoreceptors, rp=retinal plexus, scn=supporting cell nuclei, arrowheads peripherically thickened eye cartilage
Fig. 9 in Comparative 3D microanatomy and histology of the eyes and central nervous systems in coleoid cephalopod hatchlings
Fig. 9 Comparative histology of the central nervous system II (transversal sections at the level of brachio-pedal connectives). a Sepia officinalis (Richardson), b Rossia macrosoma (Azan), c Sepietta obscura (Azan), d Idiosepius notoides (Richardson), e Loligo vulgaris (Richardson), f Octopus vulgaris (Azan). Labels: bpc=connectivum brachio- pedale, bpvc=connectivum brachio-pallioviscerale, nas=superior antorbital nerve, noa=anterior oculomotoric nerve, noai= inferior anterior oculomotoric nerve, nopa=anterior inferior ophthalmic nerve, pbrl=posterior brachial lobe
Fig. 12 in Comparative 3D microanatomy and histology of the eyes and central nervous systems in coleoid cephalopod hatchlings
Fig. 12 Rossia macrosoma hatchling: histology of the head region (transversal sections; Trichrome de Masson staining, except f: Azan staining; see also interactive supplementary figure 2). a Overview with selected planes B-H (3D reconstruction; left side view). b Base of brachial crown with arms and tentacles. c Base of brachial crown with buccal mass. d Midline of eyes, radula. e Central lobus opticus just behind the eyes. f Central lobus opticus with optic commissure. g Posterior lobus opticus, statocysts with statoliths. h Palliovisceral lobes just at the end of the optic lobes. Labels: a 1– 4=arms 1–4, aco=anterior chamber organ, bm=buccal mass, es= esophagus, ey=eye, fu=funnel, ibl=inferior buccal lobe, ifl=inferior frontal lobe, le=lens, mcl=magnocellular lobe, oc=optic commissure, ofl= olfactory lobe, ol=optic lobe (medullar core), opl=outer plexiform layer, pdl=peduncle lobe, pl=pedal lobe, pvl=palliovisceral lobe, ra=radula, re=retina, sl= statolith, st=statocyst, t=tentacle, tp=tentacular pocket, vtl=vertical lobe, ys=yolk sac
Fig. 3 in Comparative 3D microanatomy and histology of the eyes and central nervous systems in coleoid cephalopod hatchlings
Fig. 3 Comparative eye histology (transversal sections through lens centers; surface renderings of left retinae—not true to scale; gray arrowhead pointing rostrally). a Sepia officinalis (Richardson), b Rossia macrosoma (Trichrome de Masson), c Sepietta obscura (Trichrome de Masson), d Idiosepius notoides (Richardson), e Loligo vulgaris (Richardson), f Octopus vulgaris (Azan). Labels: aco=anterior chamber organ, cb=ciliary body, co=cornea, ir=iris, le=lens, ol=optic lobe, on=optic nerve, re=retina, arrows: septum, black arrowheads: lids
Fig. 1 Midsagittal section through a in Comparative 3D microanatomy and histology of the eyes and central nervous systems in coleoid cephalopod hatchlings
Fig. 1 Midsagittal section through a cephalopod-coleoid central nervous system with its main neuropils (Loligo vulgaris). a Profiles of subesophageal and supraesophageal masses with neuropils (light gray) and perikaryal layers (dark gray)(compare, e.g., with Novicki et al. 1990, Fig. 14). b Digital YZ-reslice with labeled neuropils (2D). c Digital YZ-reslice with labeled neuropils (3D, same colors as in b). Labels: abl=anterior basal lobe, bl=brachial lobe, dbl=dorsal basal lobe, es=esophagus, ifl=inferior frontal lobe, mbl=median basal lobe, pcl=precommissural lobe, pdc=peduncle commissure, pl= pedal lobe, pvl=palliovisceral lobe, sfl=superior frontal lobe, svl= subvertical lobe, vtl=vertical lobe
Fig. 4 a –e in 3D-microanatomy and histology of the hydrothermal vent gastropod Lurifax vitreus Warén & Bouchet, 2001 (Heterobranchia: Orbitestellidae) and comparisons with Ectobranchia
Fig. 4 a –e Histological images of the genital system of L. vitreus. a 3D-reconstruction of the genital system, view from left. b Hermaphroditic gland with border of testis and ovary compartments (arrowheads). c Gonoduct with four differently stained glandular epithelia. d Base of penis with sperm groove. e Penis depicted in volume rendering mode (see Materials and methods) showing the seminal groove (dark red). I –IV Different sorts of glandular epithelia, eg egg, n nucleus, pe penis, pt pallial tentacle, sgr sperm groove, sp sperm, ► border of ovary and testis compartments. Bars b, d 50 μm; c 100 μm
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