iiinova — where your digital self keeps evolving

Moritz Negwer @moritz-negwer.mstdn.science.ap.brid.gy · 16/09/2026

Proud to announce our Tissue Clearing & Light-sheet microscopy seminar on Thursday 24th (next week!) in Nijmegen, that we organized together with Gert-Jan Bakker and Miltenyi Biotec. Come to see what you can learn from organoids up until entire mice! We'll […] [Original post on mstdn.science]

Flyer for the tissue clearing workshop described in the post

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Moritz Negwer @moritz-negwer.mstdn.science.ap.brid.gy · 08/09/2026

Neat detail: the window coating has small gaps patterned with what looks like Voronoi tessellation (faint blue). I guess this is where the internet gets in!

Angled close-up shot of the train window, focusing on raindrops on the glass with a gray overcast sky as backdrop. The window has a blue-ish coating that has gaps with a semi-regular hexagonal pattern. It looks a bit like Voronoi tessellation. Presumably the gaps are to render the windows transparent for cellphone frequencies.

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Moritz Negwer @moritz-negwer.mstdn.science.ap.brid.gy · 04/08/2026

Do you already have cleared-brain image stacks, but don't know what to do with them? Or maybe you want to learn which parameters are important before embarking on an imaging campaign? In this intensive 2-day hands-on workshop you will learn how to handle 3D […] [Original post on mstdn.science]

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Moritz Negwer @moritz-negwer.mstdn.science.ap.brid.gy · 21/06/2026

Ikea's cephalopod-shaped footwear-drying accessory is cheap and useful. But, why did they name it "Bressa" when "Socktopus" was *right there*? #ikea #dadjoke

A clothesdryer accesory in the shape of an octopus that can clip 16 socks. Why did Ikea not name it Socktopus? Image from the Ikea website, because our own looks way messier.

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Moritz Negwer @moritz-negwer.mstdn.science.ap.brid.gy · 19/10/2025

This week I had the pleasure of attending the hashtag#MesoSPIM Symposium in Zürich, Switzerland - and what an experience it's been! Top-notch presentations, great posters and great chats with my fellow #lightsheet #microscopy and #tissueclearing nerds. You know […] [Original post on mstdn.science]

Moritz in front of his poster presentation at the MesoSPIM Symposium in Zürich, Switzerland

Me in front of the ÖBB Nightjet sleeper train carriage that took me to Zürich and back. Surprisingly comfortable if you book the sleeper wagon with the nice beds!

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Moritz Negwer @moritz-negwer.mstdn.science.ap.brid.gy · 06/08/2025

Spotted: assorted #Mosstodon and #LichenSubscribe growing on top of a house-style bird feeder, in a layer thicker than the original roof.

A thicket of various mosses and lichens growing on top of an old wooden bird feeder

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Moritz Negwer @moritz-negwer.mstdn.science.ap.brid.gy · 19/05/2025

@SafeguardingResearch @hazel 24) To automatically keep downloading any torrent that gets added to the RSS feed, click "RSS Downloader" on the very right side. Then, create a new rule by clicking the blue + in the pop-up. Then select the new rule, check the […] [Original post on mstdn.science]

Screenshot of the qbittorrent-nox webUI explaining how to make an auto-download rule for RSS feeds

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Moritz Negwer @moritz-negwer.mstdn.science.ap.brid.gy · 19/05/2025

@SafeguardingResearch @hazel 22) Then click on the RSS logo to the very right side at the top of the web interface. This takes you to the RSS reader. 23) Click on the "New Subscription" button on the left. Then, paste the RSS feed link from […] [Original post on mstdn.science]

Screenshot of the qbittorrent-nox webUI with annotations explaining how to open the RSS reader

Screenshot of the qbittorrent-nox webUI with annotations explaining how to add an RSS feed

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Moritz Negwer @moritz-negwer.mstdn.science.ap.brid.gy · 19/05/2025

@SafeguardingResearch @hazel 23) In the qbittorrent webUI, go to Settings -> RSS, and check the "Enable fetching of RSS feeds" and "Enable auto-downloading of RSS torrents" checkboxes. Don't forget to hit Save to make the changes stick.

screenshot of the qbittorrent-nox web interface with annotations explaining how to auto-download RSS feeds

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Moritz Negwer @moritz-negwer.mstdn.science.ap.brid.gy · 19/05/2025

@SafeguardingResearch 21) Much easier way to add torrents via RSS feeds, with thanks to @hazel for pointing this out. This is adapted from the following guide: www.makeuseof.com/tag/how-to-use-rs… […] [Original post on mstdn.science]

screenshot of https://sciop.net/feeds with annotations

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Moritz Negwer @moritz-negwer.mstdn.science.ap.brid.gy · 18/05/2025

@SafeguardingResearch 20) Optional optimalizations: If you want to change the web interface password, go to Settings -> WebUI and filling in the new user/password combo. Don't forget to scroll down and click "Save" to make the changes stick.

Screenshot of the qbittorrent-nox web ui showing how to change the login credentials to the web ui

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Moritz Negwer @moritz-negwer.mstdn.science.ap.brid.gy · 18/05/2025

@SafeguardingResearch 19) Optional optimalizations: If you want to change upload/download max speed, click the Settings symbol -> Speed -> Upload/Download speed. The speed is set to a rather high 50 MByte/s, i.e. slightly less than half a Gigabit connection […] [Original post on mstdn.science]

Screenshot of the qbittorrent-nox web interface with instructions on how to change the up-/download speed limits

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Moritz Negwer @moritz-negwer.mstdn.science.ap.brid.gy · 18/05/2025

@SafeguardingResearch 16) Back on the web interface, click File -> Add a torrent link and paste the magnet link into the box. You can add several magnet links at once if you enter each on a new line (=hit Enter between links). 17) Scroll down and press the […] [Original post on mstdn.science]

Screenshot of the qbittorrent-nox web interface with explainer text pointing out the "add a torrent via link" function

Screenshot of the qbittorrent-nox web interface with explainer text pointing out where to paste the magnet link

Screenshot of the qbittorrent-nox web interface with explainer text pointing out the Download button

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Moritz Negwer @moritz-negwer.mstdn.science.ap.brid.gy · 18/05/2025

@SafeguardingResearch 15) Add a torrent by copying the magnet link from sciop.net. You can sort the datasets by endangerment or by the number of other people seeding it. sciop.net/datasets/?sort=-threat Pick a dataset, right-click on the blue magnet and copy the link.

Screenshot of the qbittorrent-nox web interface with explainer text pointing out various functions

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Moritz Negwer @moritz-negwer.mstdn.science.ap.brid.gy · 18/05/2025

@SafeguardingResearch 13) The web interface should look like this. 14) Enter your credentials into the web interface, it should look like this. Per the configuration in step 7, the credentials should be as follows: name: sciop password: safeguardingresearch […] [Original post on mstdn.science]

Screenshot of the qBittorrent-nox webUI with credentials sciop / safeguardingresearch

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Moritz Negwer @moritz-negwer.mstdn.science.ap.brid.gy · 09/04/2025

Here's an interesting way to do photobleaching with cleared tissue: Add 0.1% H2O2 to the clearing medium and blast with LEDs for 24h at RT. Also includes very detailed instructions for building an LED photobleaching setup - the samples ate placed between two […] [Original post on mstdn.science]

Figure 5 | Application of the photobleacher to the pigment-rich volumetric tissues after clearing. (A) Schematic illustration of the photobleaching process. The tissues were illuminated after clearing, with hydrogen peroxide included when necessary. (B) Mouse hearts with various photobleaching conditions. Representative single z-planes are shown. (C) Three-dimensional rendering of a mouse heart after IHC staining using an anti-αSMA antibody. (D) Pieces of human cortex from an identical donor, with various photobleaching conditions. Three-dimensional renderings are shown. Outlines of tissues were shown in dot lines when necessary. (E) Three-dimensional rendering of a human cerebral cortex after IHC staining using anti-αSMA and anti-GFAP antibodies.

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Moritz Negwer @moritz-negwer.mstdn.science.ap.brid.gy · 13/03/2025

3500 people protesting the right-wing Dutch government's 1.3 billion € budget cuts to higher education. This is an extinction-level event for dutch research, and @Radboud_uni @radboudumc and the HAN are having none of it. #nijmegen #woinactie #doehetniet

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Moritz Negwer @moritz-negwer.mstdn.science.ap.brid.gy · 27/02/2025

I just stumbled on this Raspi-based video camera + video editing thing and haven't seen it mentioned here. Looks pretty complete and has a #functional3dprint case, #foss software, #openhardware interface and is easily maintainable. Looks cool, anyone tried it […] [Original post on mstdn.science]

An image showing a 3-d printed orange/black camera with a long objective.

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Moritz Negwer @moritz-negwer.mstdn.science.ap.brid.gy · 07/02/2025

New publication from Kwanhun Chung lab at MIT improves on their SWITCH approach and eFLASH stochastic electrotransport to improve antibody labeling by gradually shifting the microenvironment. Looks interesting, I wonder how well it can be adapted to other […] [Original post on mstdn.science]

Fig. 4: Holistic comparison of transgenic and immunolabeling-based cell type labeling. a–c, 3D dataset from a PV-Cre and loxP-tdTomato dual transgenic mouse hemisphere stained with anti-PV antibody. a, Representative optical section. b, Magnified images of a. c, A percentage plot for tdTomato-only (red), anti-PV-only (green) and tdTomato and anti-PV co-positive cells (yellow) among all the labeled cells in individual representative brain regions. d–h, 3D dataset of a ChATBAC-eGFP mouse brain stained with anti-ChAT antibody. d, Whole volume rendering. e, Magnified images of d. f, A percentage plot for EGFP-only (green), anti-ChAT-only (red) and EGFP and anti-ChAT co-positive cells (yellow) among all the labeled cells in individual representative brain regions. g, Magnified view of d. h, Zoom-in view of g. Scale bars, 2 mm (cyan) and 200 μm (white). 5N, motor nucleus of trigeminal; A1, primary auditory cortex; AC, anterior cingulate cortex; BLAa, basolateral amygdala, anterior part; BLAp, basolateral amygdala, posterior part; CA1, hippocampal CA1; CA3, hippocampal CA3; CeA, central amygdala; DG, dentate gyrus; dNAmb, nucleus ambiguus, dorsal part; Ecto, ectorhinal cortex; LA, lateral amygdala; lEnto, lateral entorhinal cortex; mo, dentate gyrus, molecular layer; po, dentate gyrus, polymorph layer; Piri, piriform cortex; PPA, posterior parietal association cortex; RSA, retrosplenial cortex; sg, dentate gyrus, granule cell layer; V1, primary visual cortex;

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Moritz Negwer @moritz-negwer.mstdn.science.ap.brid.gy · 03/02/2025

Whole-mouse imaging the hard way: Clearing, then slicing + block-face imaging with beam-scan / sensor scan-line synchronization and continuous stage movement in an oblique imaging setup (ViSOR). This time, they scaled it up to whole-mouse and used pre-cleared […] [Original post on mstdn.science]

Figure 1. ARCHmap-blockface-VISoR approach for high-throughput mapping of whole mouse body at micron resolution

(A) ARCHmap-blockface-VISoR pipeline for whole-mouse imaging.

(B) Bright-field view of a cleared 2-month-old vGAT-Cre;Ai14 mouse and 400-μm-thick sections collected during blockface imaging.

(C) 3D view of a ∼600-μm-thick thoracic volume imaged from a blockface imaging section.

(C1-C6) Representative high-resolution images showing maximum intensity projection of 20-μm-thick stacks in (C) at depths of 100 μm (C1, zoomed-in view in C4), 300 μm (C2, zoomed-in view in C5), and 600 μm (C3, zoomed-in view in C6).

(D, D1) Blockface-VISoR setup. (D1) Magnification of the imaging region in (D).

(E) Cross section of imaging and sectioning modules of the blockface-VISoR setup.

(F) Schematic showing overlapped imaging data (pink) of ∼200-µm thickness between 2 contiguous imaging sections.

(G) Comparison of 3D intersection alignment by natural coordinates (G1) and a custom 3D reconstruction method (G2). Images of vessel fluorescence are the maximum intensity y-projection of 20-µm-thick sections in the upper section (red) and the lower section (green).

(H) 3D view of nerve and vasculature in a whole adult Thy1-EGFP mouse. Red hot (black-red-yellow-light yellow spectrum), LEL-DL649; cyan hot (black-blue-cyan-white spectrum), Thy1-EGFP; white surface, whole mouse.

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Moritz Negwer @moritz-negwer.mstdn.science.ap.brid.gy · 31/01/2025

New deep-learning cell detection pipeline for light-sheet mouse brain image stacks, with an interesting cell-coordinate clustering statistics approach: A deep learning pipeline for three-dimensional brain-wide mapping of local neuronal ensembles in teravoxel […] [Original post on mstdn.science]

Fig. 1 a–c, Intact whole brains immunolabeled, cleared and imaged with LSFM were used as input to the ACE pipeline. a, Whole-brain LSFM data are passed to ACE’s segmentation module, consisting of ViT- and CNN-based DL models, to generate binary segmentation maps in addition to a voxel-wise uncertainty map for estimation of model confidence. b, The autofluorescence channel of data is passed to the registration module, consisting of MIRACL registration algorithms, to register to a template brain such as the Allen Mouse Brain Reference Atlas (ARA). High-resolution segmentation maps are then voxelized using a convolution filter and warped to the ARA (10 µm) using deformations obtained from registration. c, Voxelized and warped segmentation maps are passed to ACE’s statistics module. Group-wise heatmaps of neuronal density are obtained by subtracting the average of warped and voxelized segmentation maps in each group to identify neural activity hotspots. To identify significant localized group-wise differences in neuronal activity in an atlas-agnostic manner, a cluster-wise, threshold-free cluster enhancement permutation analysis (using group-wise ANOVA) is conducted. The resulting P value map represents clusters showing significant differences between groups. Correspondingly, ACE outputs a table summarizing these clusters, including their volumes and the portion of each brain region included in each cluster.

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Moritz Negwer @moritz-negwer.mstdn.science.ap.brid.gy · 26/12/2024

Cool custom-built #lightsheet #microscopes: Turns out you can build a tiny light-sheet projector by whipping an optical fiber back and forth in front of a GRIN lens. The entire assembly is hand-made (coils, magnet, casing) and fits into an 18G needle. This […] [Original post on mstdn.science]

Fig. 2 of the paper. It shows three views of the optics construction. Left, an illustration of the principle. An optical fiber is swing back and forth in a hollow tube with a lens at the end, with the beam being projecting to different points in space.
Middle and right, two views of the detailed construction of the optics. Tiny hand-wound coils are glued to the fiber and move it towards or away from magnets (manually ground to size) at the tube wall. Two sets of coils and magnets move the fiber in the X and Y axis. At the end of the tube, the beam is focused by a GRIN lens and aimed sideways via a prism.

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Moritz Negwer @moritz-negwer.mstdn.science.ap.brid.gy · 25/11/2024

20k people protesting against the draconian > 1 billion € cuts to the dutch education system, filling the Malieveld in The Hague. You know that the right-wing government messed up when this is opposed by students, university boards, the heads of the […] [Original post on mstdn.science]

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Moritz Negwer @moritz-negwer.mstdn.science.ap.brid.gy · 24/11/2024

Wow, TRISCO (née TRIC-DISCO) is out in Science! This cool approach allows imaging of mRNA transcripts throughout the cleared mouse brain. It uses a signal amplification step with in situ Hybridization Chain Reaction (isHCR) and combines it with DISCO-style […] [Original post on mstdn.science]

Fig. 3. Multiplexed TRISCO staining of whole brains.
(A) Schematic of the TRISCO protocol spanning 15 days. (B) (Top) 3D rendering of the whole brain from an 8-week-old adult mouse stained using TRISCO for cortical interneuron transcripts: Somatostatin (Sst mRNA, red), Parvalbumin (Pvalb mRNA, green), and Glutamate decarboxylase 1 (Gad1 mRNA, blue). (Bottom) Single-channel views. Bounding box, 7.7 × 10.6 × 5.5 mm. (C) Optical cross section at z = 2875 μm of the TRISCO brain in (B). (Right) Single-channel views. (Bottom) Magnified views of the hippocampus region at the indicated box. Nuclear staining was done with DiYO-1. Scale bars, 1 mm (white) and 200 μm (yellow).

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Moritz Negwer @moritz-negwer.mstdn.science.ap.brid.gy · 19/11/2024

New #microglia #morphology analysis pipeline. Looks useful! MorphoCellSorter: An Andrews plot-based sorting approach to rank microglia according to their morphological features Benkeder et al., reviewed preprint at eLife 2024 […] [Original post on mstdn.science]

k-means clustering identifies highly different populations contralaterally vs ipsilaterally in an ischemic stroke model but offers a heterogeneous cluster composition.

A T2-weighted MRI acquisition of the tMCAO rat brain 24 hours after reperfusion (top). Z maximum projections of IBA1 staining of microglia on the ipsilateral side to the lesion (bottom left) and contralateral side (bottom right). Scale bar: 20 µm. B Scatter plot with each dot representing one microglia from the complete dataset (ipsilateral and contralateral), plotted in function of their PC1 against PC2 values from the PCA conducted on all 20 initial morphological parameters. The colors represent the clusters identified by the k-means method, and the ‘x’ symbols are the centers of each cluster. C All microglia from the dataset with colors associated to their affiliated cluster: green corresponds to cluster 1 (ramified microglia), blue corresponds to cluster 2 (activated microglia), yellow corresponds to cluster 3 (amoeboid microglia) and pink to cluster 4 (rod-like microglia). The white crosses indicate cells that exhibit morophological characteristics that should categorize them in another cluster. D Pie chart illustrating the proportion of each cluster constituting the contralateral and ipsilateral sides.

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Moritz Negwer @moritz-negwer.mstdn.science.ap.brid.gy · 23/04/2024

Very excited that our whole-mouse-brain analysis pipeline - DELiVR - is published now at Nature Methods. With DELiVR, we built an open-source, easy-to-use pipeline for analyzing image stacks from cleared mouse brains. Paper […] [Original post on mstdn.science]

Fig. 1 about DELiVR:
Step 1: Tissue clearing, light-sheet microscopy
Step 2: Generate custom training data in VR
Step 3: run the analysis pipeline with the custom-trained deep-learning model inside the dockerized DELiVR pipeline

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